From d8e2b89c30bbdbb61a96e074db0f598b08f34053 Mon Sep 17 00:00:00 2001
From: Ty Kay <kay@wm6d8-674.broadinstitute.org>
Date: Wed, 2 Aug 2023 09:42:40 -0400
Subject: [PATCH 1/5] creates multiple enginges to handle different ploidies

Finish changes to HaplotypeCaller to add ploidy-regions flag allowing variable ploidy

Change IntervalFileFeature interface to NamedFeature for htsjdk dependency

Address comments for draft PR

Make a few changes and refactors based on comments

Add some tests and small tweaks
---
 .../formats/records/SimpleCount.java          |  14 +-
 .../haplotypecaller/HaplotypeCaller.java      |  15 +
 .../HaplotypeCallerArgumentCollection.java    |  25 +-
 .../HaplotypeCallerEngine.java                | 160 ++++++++--
 .../RampedHaplotypeCallerEngine.java          |   8 +-
 .../HaplotypeCallerIntegrationTest.java       | 117 ++++++++
 .../expected.testPloidyRegions.vcf            | 273 ++++++++++++++++++
 .../testMismatchPloidyRegions.bed             |   3 +
 .../testNegativePloidyRegions.bed             |   3 +
 .../testNonIntegerPloidyRegions.bed           |   3 +
 .../haplotypecaller/testPloidyRegions.bed     |   4 +
 11 files changed, 603 insertions(+), 22 deletions(-)
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testPloidyRegions.vcf
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testMismatchPloidyRegions.bed
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNegativePloidyRegions.bed
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNonIntegerPloidyRegions.bed
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testPloidyRegions.bed

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java
index 5d6521850b5..bdf70dc5ccf 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java
@@ -2,6 +2,8 @@
 
 import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.Feature;
+import htsjdk.tribble.NamedFeature;
+import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.param.ParamUtils;
@@ -19,7 +21,17 @@ public class SimpleCount implements Locatable, Feature {
     public SimpleCount(final SimpleInterval interval,
                        final int count) {
         this.interval = Utils.nonNull(interval);
-        this.count = ParamUtils.isPositiveOrZero(count, "Can't construct SimpleCount with negative count.");
+        this.count = ParamUtils.isPositiveOrZero(count, "Can't construct SimpleCount with negative count at " + interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd() + ".");
+    }
+
+    public SimpleCount(final NamedFeature namedFeature) {
+        try {
+            int count = Integer.parseInt(namedFeature.getName());
+            this.interval = new SimpleInterval(namedFeature);
+            this.count = ParamUtils.isPositiveOrZero(count, "Can't construct SimpleCount with negative count at " + namedFeature.getContig() + ":" + namedFeature.getStart() + "-" + namedFeature.getEnd() + ".");
+        } catch (NumberFormatException e) {
+            throw new IllegalArgumentException("Error parsing name into integer for feature at " + namedFeature.getContig() + ":" + namedFeature.getStart() + "-" + namedFeature.getEnd() + ".");
+        }
     }
 
     @Override
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java
index f504d400b13..557e7f0add9 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -127,6 +127,21 @@
  * argument. Note however that very high ploidies (such as are encountered in large pooled experiments) may cause
  * performance challenges including excessive slowness. We are working on resolving these limitations.</p>
  *
+ * <p>For having variable ploidy in different regions, like making haploid calls outside the PAR on chrX or chrY,
+ * see the --ploidy-regions flag. The -ploidy flag sets the default ploidy to use everywhere, and --ploidy-regions
+ * should be a .bed or .interval_list with "name" column containing the desired ploidy to use in that region
+ * when genotyping. Note that variants near the boundary may not have the matching ploidy since the ploidy used will
+ * be determined using the following precedence: </p>
+ * <ol>
+ *     <li>ploidy given in --ploidy-regions for all intervals overlapping the active region when calling your variant
+ *     (with ties broken by using largest ploidy); note ploidy interval may only overlap the active region and determine
+ *     the ploidy of your variant even if the end coordinate written for your variant lies outside the given region;</li>
+ *     <li>ploidy given via global -ploidy flag;</li>
+ *     <li>ploidy determined by the default global built-in constant for humans (2).</li>
+ * </ol>
+ *
+ * <p>Coordinates for the PAR for CRCh38 can be found <a href='http://useast.ensembl.org/info/genome/genebuild/human_PARS.html'>here</a>.</p>
+ *
  * <h3>Additional Notes</h3>
  * <ul>
  *     <li>When working with PCR-free data, be sure to set `-pcr_indel_model NONE` (see argument below).</li>
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
index 7ab58d73264..4ba22493c03 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
@@ -1,6 +1,8 @@
 package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
 
+import htsjdk.tribble.NamedFeature;
 import htsjdk.variant.variantcontext.VariantContext;
+import org.apache.arrow.util.VisibleForTesting;
 import org.apache.commons.lang3.ArrayUtils;
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
@@ -9,6 +11,7 @@
 import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection;
+import org.broadinstitute.hellbender.engine.FeatureDataSource;
 import org.broadinstitute.hellbender.engine.FeatureInput;
 import org.broadinstitute.hellbender.engine.GATKPath;
 import org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection;
@@ -23,9 +26,11 @@
 /**
  * Set of arguments for the {@link HaplotypeCallerEngine}
  */
-public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgumentCollection implements Serializable{
+public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgumentCollection implements Serializable {
     private static final long serialVersionUID = 1L;
 
+    public static final String PLOIDY_REGIONS_NAME = "ploidy-regions";
+
     public static final String GQ_BAND_LONG_NAME = "gvcf-gq-bands";
     public static final String GQ_BAND_SHORT_NAME = "GQB";
     public static final String DO_NOT_CORRECT_OVERLAPPING_BASE_QUALITIES_LONG_NAME = "do-not-correct-overlapping-quality";
@@ -61,6 +66,9 @@ protected ReadThreadingAssemblerArgumentCollection getReadThreadingAssemblerArgu
         return new HaplotypeCallerReadThreadingAssemblerArgumentCollection();
     }
 
+    @Argument(fullName = PLOIDY_REGIONS_NAME, shortName = PLOIDY_REGIONS_NAME, doc = "Interval file with column specifying desired ploidy for genotyping models. Overrides default ploidy and user-provided --ploidy argument in specific regions.", optional = true)
+    public FeatureDataSource<NamedFeature> ploidyRegions = null;
+
     /**
      * You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This
      * is especially useful if your samples are all in the same file but you need to run them individually through HC
@@ -312,6 +320,21 @@ boolean isFlowBasedCallingMode() {
         return flowMode != FlowMode.NONE;
     }
 
+    // Default constructor
+    public HaplotypeCallerArgumentCollection() {
+        super();
+    }
+
+    // Private constructor for use in copyWithNewPloidy
+    // Allows you to make new instances of hcArgs with identical fields except for genotyper ploidy
+    private HaplotypeCallerArgumentCollection(int ploidy) {
+        this.standardArgs.genotypeArgs.samplePloidy = ploidy;
+    }
+
+    // Copy method used to create new hcArgs with same fields except input ploidy model
+    public HaplotypeCallerArgumentCollection copyWithNewPloidy(int ploidy) {
+        return new HaplotypeCallerArgumentCollection(ploidy);
+    }
 
     /**
      * the different flow modes, in terms of their parameters and their values
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
index 71f6d64ede7..0126a49b802 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
@@ -3,7 +3,10 @@
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
+import htsjdk.samtools.util.Locatable;
+import htsjdk.samtools.util.OverlapDetector;
 import htsjdk.samtools.util.RuntimeIOException;
+import htsjdk.tribble.NamedFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
@@ -20,12 +23,15 @@
 import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter;
 import org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection;
 import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
 import org.broadinstitute.hellbender.tools.walkers.annotator.*;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
+import org.broadinstitute.hellbender.utils.IntervalUtils;
 import org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.hellbender.utils.haplotype.Event;
 import org.broadinstitute.hellbender.utils.pileup.PileupBasedAlleles;
@@ -83,8 +89,31 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
 
     protected final OutputStreamWriter assemblyDebugOutStream;
 
-    // the genotyping engine for the isActive() determination
-    private MinimalGenotypingEngine activeRegionEvaluationGenotyperEngine = null;
+    /**
+     * List of interval file entries including regions and custom ploidy values to apply in that region.
+     */
+    protected final List<SimpleCount> ploidyRegions = new ArrayList<>();
+
+    /**
+     * An OverlapDetector object for checking whether region overlaps given ploidyRegions.
+     */
+    protected final OverlapDetector<SimpleCount> ploidyRegionsOverlapDetector;
+
+    /**
+     * List of all custom ploidies provided by user
+     */
+    private final LinkedHashSet<Integer> allCustomPloidies;
+
+    /**
+     * The default genotyping engine for the isActive() determination
+     */
+    private MinimalGenotypingEngine defaultActiveRegionEvaluationGenotyperEngine = null;
+
+    /**
+     * Map of user-provided ploidy values to corresponding active region genotyper. Values are checked as valid Integers during
+     * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
+     */
+    private final HashMap<Integer, MinimalGenotypingEngine> ploidyToActiveEvaluationGenotyper = new HashMap<>();
 
     protected ReadThreadingAssembler assemblyEngine = null;
 
@@ -93,7 +122,16 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
     // If we are in PDHMM mode we need to hold onto two likelihoods engines for the fallback
     private ReadLikelihoodCalculationEngine pdhmmLikelihoodCalculationEngine = null;
 
-    protected HaplotypeCallerGenotypingEngine genotypingEngine = null;
+    /**
+     * The default genotyping engine to use for actual variant calling and genotyping in an active region.
+     */
+    protected HaplotypeCallerGenotypingEngine defaultGenotypingEngine = null;
+
+    /**
+     * Map of user-provided ploidy values to corresponding genotyper. Values are checked as valid Integers during
+     * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
+     */
+    protected final HashMap<Integer, HaplotypeCallerGenotypingEngine> ploidyToGenotyperMap = new HashMap<>();
 
     private VariantAnnotatorEngine annotationEngine = null;
 
@@ -163,7 +201,7 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
     /**
      * Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header,
      * and a reference file
-     *  @param hcArgs command-line arguments for the HaplotypeCaller
+     * @param hcArgs command-line arguments for the HaplotypeCaller
      * @param assemblyRegionArgs
      * @param createBamOutIndex true to create an index file for the bamout
      * @param createBamOutMD5 true to create an md5 file for the bamout
@@ -196,6 +234,20 @@ public HaplotypeCallerEngine(final HaplotypeCallerArgumentCollection hcArgs, Ass
             HaplotypeCallerGenotypingDebugger.initialize(hcArgs.genotyperDebugOutStream);
         }
 
+        // Parse the user provided custom ploidy regions into ploidyRegions object containing SimpleCounts
+        if (this.hcArgs.ploidyRegions != null) {
+            this.hcArgs.ploidyRegions.forEach(r -> this.ploidyRegions.add(new SimpleCount(r)));
+        }
+
+        for (SimpleCount region : this.ploidyRegions) {
+            if (!IntervalUtils.intervalIsOnDictionaryContig(region.getInterval(), readsHeader.getSequenceDictionary())) {
+                throw new UserException("Invalid region provided for --ploidy-regions at " + region.getContig() + ":" + region.getStart() + "-" + region.getEnd() + ". Contig name or endpoint doesn't match read sequence dictionary.");
+            }
+        }
+
+        this.ploidyRegionsOverlapDetector = OverlapDetector.create(this.ploidyRegions);
+        this.allCustomPloidies = this.ploidyRegions.stream().map(SimpleCount::getCount).collect(Collectors.toCollection(LinkedHashSet::new));
+
         trimmer = new AssemblyRegionTrimmer(assemblyRegionArgs, readsHeader.getSequenceDictionary());
         initialize(createBamOutIndex, createBamOutMD5);
     }
@@ -242,8 +294,16 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5
 
         initializeActiveRegionEvaluationGenotyperEngine();
 
-        genotypingEngine = new HaplotypeCallerGenotypingEngine(hcArgs, samplesList, ! hcArgs.doNotRunPhysicalPhasing, hcArgs.applyBQD);
-        genotypingEngine.setAnnotationEngine(annotationEngine);
+        defaultGenotypingEngine = new HaplotypeCallerGenotypingEngine(hcArgs, samplesList, ! hcArgs.doNotRunPhysicalPhasing, hcArgs.applyBQD);
+        defaultGenotypingEngine.setAnnotationEngine(annotationEngine);
+
+        // Create other custom genotyping engines if user provided ploidyRegions
+        for (final int ploidy : this.allCustomPloidies) {
+            HaplotypeCallerArgumentCollection newPloidyHcArgs = hcArgs.copyWithNewPloidy(ploidy);
+            HaplotypeCallerGenotypingEngine newGenotypingEngine = new HaplotypeCallerGenotypingEngine(newPloidyHcArgs, samplesList, ! hcArgs.doNotRunPhysicalPhasing, hcArgs.applyBQD);
+            newGenotypingEngine.setAnnotationEngine(annotationEngine);
+            this.ploidyToGenotyperMap.put(ploidy, newGenotypingEngine);
+        }
 
         boolean isFlowBased = (hcArgs.likelihoodArgs.likelihoodEngineImplementation == ReadLikelihoodCalculationEngine.Implementation.FlowBased)
                 || (hcArgs.likelihoodArgs.likelihoodEngineImplementation == ReadLikelihoodCalculationEngine.Implementation.FlowBasedHMM);
@@ -381,8 +441,18 @@ private void initializeActiveRegionEvaluationGenotyperEngine() {
         // Seems that at least with some test data we can lose genuine haploid variation if we use ploidy == 1
         activeRegionArgs.genotypeArgs.samplePloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, hcArgs.standardArgs.genotypeArgs.samplePloidy);
 
-        activeRegionEvaluationGenotyperEngine = new MinimalGenotypingEngine(activeRegionArgs, samplesList);
-        activeRegionEvaluationGenotyperEngine.setLogger(logger);
+        defaultActiveRegionEvaluationGenotyperEngine = new MinimalGenotypingEngine(activeRegionArgs, samplesList);
+        defaultActiveRegionEvaluationGenotyperEngine.setLogger(logger);
+
+        // If custom ploidyRegions provided, create corresponding map for active region determination genotyper
+        for (final int ploidy : this.allCustomPloidies) {
+            StandardCallerArgumentCollection newPloidyActiveArgs = new StandardCallerArgumentCollection();
+            newPloidyActiveArgs.copyStandardCallerArgsFrom(activeRegionArgs);
+            newPloidyActiveArgs.genotypeArgs.samplePloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, ploidy);
+            MinimalGenotypingEngine newActiveGenotypingEngine = new MinimalGenotypingEngine(newPloidyActiveArgs, samplesList);
+            newActiveGenotypingEngine.setLogger(logger);
+            this.ploidyToActiveEvaluationGenotyper.put(ploidy, newActiveGenotypingEngine);
+        }
     }
 
     /**
@@ -455,7 +525,7 @@ public VCFHeader makeVCFHeader( final SAMSequenceDictionary sequenceDictionary,
         final Set<VCFHeaderLine> headerInfo = new HashSet<>();
         headerInfo.addAll(defaultToolHeaderLines);
 
-        headerInfo.addAll(genotypingEngine.getAppropriateVCFInfoHeaders());
+        headerInfo.addAll(defaultGenotypingEngine.getAppropriateVCFInfoHeaders());
         // all annotation fields from VariantAnnotatorEngine
         headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions(emitReferenceConfidence()));
         // all callers need to add these standard annotation header lines
@@ -523,6 +593,57 @@ public void writeHeader( final VariantContextWriter vcfWriter, final SAMSequence
         vcfWriter.writeHeader(makeVCFHeader(sequenceDictionary, defaultToolHeaderLines));
     }
 
+    /**
+     * Determines the appropriate ploidy to use at given site for different genotyping engines.
+     * @param region Current region of interest
+     * @return Ploidy value to use here given user inputs, or -1 if fall back to default
+     */
+    private int getPloidyToUseAtThisSite(Locatable region) {
+        Set<SimpleCount> overlaps = this.ploidyRegionsOverlapDetector.getOverlaps(region);
+        // Return first engine for interval overlapping this region
+        if (!overlaps.isEmpty()) {
+            Iterator<SimpleCount> intervals = overlaps.iterator();
+            int max = intervals.next().getCount();
+            while (intervals.hasNext()) {
+                int next = intervals.next().getCount();
+                if (next > max) {
+                    max = next;
+                }
+            }
+            return max;
+        } else {
+            return -1; // Sentinel value to fall back to default genotyper
+        }
+    }
+
+    /**
+     * Selects appropriate active region genotyping engine for given region
+     * @param region Current region of interest
+     * @return Active genotyping engine with correct ploidy setting for given region
+     */
+    private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
+        int currentPloidy = getPloidyToUseAtThisSite(region);
+        if (currentPloidy == -1) {
+            return this.defaultActiveRegionEvaluationGenotyperEngine;
+        } else {
+            return this.ploidyToActiveEvaluationGenotyper.get(currentPloidy);
+        }
+    }
+
+    /**
+     * Selects appropriate genotyping engine for given region.
+     * @param region Current region of interest, e.g. AssemblyRegion
+     * @return Genotyping engine with correct ploidy setting for given region
+     */
+    protected HaplotypeCallerGenotypingEngine getLocalGenotypingEngine(Locatable region) {
+        int currentPloidy = getPloidyToUseAtThisSite(region);
+        if (currentPloidy == -1) {
+            return this.defaultGenotypingEngine;
+        } else {
+            return this.ploidyToGenotyperMap.get(currentPloidy);
+        }
+    }
+
     /**
      * Given a pileup, returns an ActivityProfileState containing the probability (0.0 to 1.0) that it's an "active" site.
      *
@@ -537,6 +658,8 @@ public void writeHeader( final VariantContextWriter vcfWriter, final SAMSequence
      */
     @Override
     public ActivityProfileState isActive(final AlignmentContext context, final ReferenceContext ref, final FeatureContext features) {
+        MinimalGenotypingEngine localActiveGenotypingEngine = getLocalActiveGenotyper(ref);
+
         if (forceCallingAllelesPresent && features.getValues(hcArgs.alleles, ref).stream().anyMatch(vc -> hcArgs.forceCallFiltered || vc.isNotFiltered())) {
             return new ActivityProfileState(ref.getInterval(), 1.0);
         }
@@ -546,7 +669,7 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
             return new ActivityProfileState(ref.getInterval(), 0.0);
         }
 
-        final int ploidy = activeRegionEvaluationGenotyperEngine.getConfiguration().genotypeArgs.samplePloidy;
+        final int ploidy = localActiveGenotypingEngine.getConfiguration().genotypeArgs.samplePloidy;
         final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy); // used to noCall all genotypes until the exact model is applied
 
         final Map<String, AlignmentContext> splitContexts;
@@ -565,7 +688,7 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
                 sample.getValue().getBasePileup().forEach(p -> PileupBasedAlleles.addMismatchPercentageToRead(p.getRead(), readsHeader, ref));
             }
             // The ploidy here is not dictated by the sample but by the simple genotyping-engine used to determine whether regions are active or not.
-            final int activeRegionDetectionHackishSamplePloidy = activeRegionEvaluationGenotyperEngine.getConfiguration().genotypeArgs.samplePloidy;
+            final int activeRegionDetectionHackishSamplePloidy = localActiveGenotypingEngine.getConfiguration().genotypeArgs.samplePloidy;
             final double[] genotypeLikelihoods = ((RefVsAnyResult) referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(
                     activeRegionDetectionHackishSamplePloidy,
                     sample.getValue().getBasePileup(), ref.getBase(),
@@ -579,9 +702,9 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
 
         if (genotypes.size() == 1) {
             // Faster implementation using exact marginalization instead of iteration
-            isActiveProb = activeRegionEvaluationGenotyperEngine.calculateSingleSampleRefVsAnyActiveStateProfileValue(genotypes.get(0).getLikelihoods().getAsVector());
+            isActiveProb = localActiveGenotypingEngine.calculateSingleSampleRefVsAnyActiveStateProfileValue(genotypes.get(0).getLikelihoods().getAsVector());
         } else {
-            final VariantContext vcOut = activeRegionEvaluationGenotyperEngine.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getEnd(), alleles).genotypes(genotypes).make());
+            final VariantContext vcOut = localActiveGenotypingEngine.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getEnd(), alleles).genotypes(genotypes).make());
             isActiveProb = vcOut == null ? 0.0 : QualityUtils.qualToProb(vcOut.getPhredScaledQual());
         }
 
@@ -607,6 +730,8 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
      * @return List of variants discovered in the region (may be empty)
      */
     public List<VariantContext> callRegion(final AssemblyRegion region, final FeatureContext features, final ReferenceContext referenceContext) {
+        final HaplotypeCallerGenotypingEngine localGenotypingEngine = getLocalGenotypingEngine(region);
+
         if ( hcArgs.justDetermineActiveRegions ) {
             // we're benchmarking ART and/or the active region determination code in the HC, just leave without doing any work
             return NO_CALLS;
@@ -799,7 +924,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
         if (hcArgs.filterAlleles) {
             logger.debug("Filtering alleles");
 
-            AlleleFilteringHC alleleFilter = new AlleleFilteringHC(hcArgs, assemblyDebugOutStream, genotypingEngine);
+            AlleleFilteringHC alleleFilter = new AlleleFilteringHC(hcArgs, assemblyDebugOutStream, localGenotypingEngine);
             //need to update haplotypes to find the alleles
             EventMap.buildEventMapsForHaplotypes(readLikelihoods.alleles(),
                     assemblyResult.getFullReferenceWithPadding(),
@@ -849,7 +974,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
             }
         }
 
-        final CalledHaplotypes calledHaplotypes = genotypingEngine.assignGenotypeLikelihoods(
+        final CalledHaplotypes calledHaplotypes = localGenotypingEngine.assignGenotypeLikelihoods(
                 haplotypes,
                 subsettedReadLikelihoodsFinal,
                 perSampleFilteredReadList,
@@ -890,7 +1015,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
 
                 result.addAll(referenceConfidenceModel.calculateRefConfidence(assemblyResult.getReferenceHaplotype(),
                         calledHaplotypes.getCalledHaplotypes(), assemblyResult.getPaddedReferenceLoc(), regionForGenotyping,
-                        subsettedReadLikelihoodsFinal, genotypingEngine.getPloidyModel(), calledHaplotypes.getCalls(), hcArgs.standardArgs.genotypeArgs.supportVariants != null,
+                        subsettedReadLikelihoodsFinal, localGenotypingEngine.getPloidyModel(), calledHaplotypes.getCalls(), hcArgs.standardArgs.genotypeArgs.supportVariants != null,
                         VCpriors));
 
                 trimmingResult.nonVariantRightFlankRegion().ifPresent(flank -> result.addAll(referenceModelForNoVariation(flank, false, VCpriors)));
@@ -948,6 +1073,7 @@ protected boolean containsCalls(final CalledHaplotypes calledHaplotypes) {
      * @return a list of variant contexts (can be empty) to emit for this ref region
      */
     protected List<VariantContext> referenceModelForNoVariation(final AssemblyRegion region, final boolean needsToBeFinalized, final List<VariantContext> VCpriors) {
+        final HaplotypeCallerGenotypingEngine localGenotypingEngine = getLocalGenotypingEngine(region);
         if ( emitReferenceConfidence() ) {
             if ( needsToBeFinalized ) {
                 AssemblyBasedCallerUtils.finalizeRegion(region,
@@ -967,7 +1093,7 @@ protected List<VariantContext> referenceModelForNoVariation(final AssemblyRegion
             final List<Haplotype> haplotypes = Collections.singletonList(refHaplotype);
             return referenceConfidenceModel.calculateRefConfidence(refHaplotype, haplotypes,
                     paddedLoc, region, AssemblyBasedCallerUtils.createDummyStratifiedReadMap(refHaplotype, samplesList, readsHeader, region),
-                    genotypingEngine.getPloidyModel(), Collections.emptyList(), hcArgs.standardArgs.genotypeArgs.supportVariants != null, VCpriors);
+                    localGenotypingEngine.getPloidyModel(), Collections.emptyList(), hcArgs.standardArgs.genotypeArgs.supportVariants != null, VCpriors);
         }
         else {
             return NO_CALLS;
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java
index b5b5c2cfa88..e47245c9f91 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java
@@ -460,6 +460,7 @@ private void uncollapse(final CallRegionContext context) {
     }
 
     private void filter(final CallRegionContext context) {
+        final HaplotypeCallerGenotypingEngine localGenotypingEngine = getLocalGenotypingEngine(context.region);
 
         try {
             // no need for this step?
@@ -479,7 +480,7 @@ private void filter(final CallRegionContext context) {
                 context.suspiciousLocations = new HashSet<>();
                 if (hcArgs.filterAlleles) {
                     logger.debug("Filtering alleles");
-                    AlleleFilteringHC alleleFilter = new AlleleFilteringHC(hcArgs, assemblyDebugOutStream, genotypingEngine);
+                    AlleleFilteringHC alleleFilter = new AlleleFilteringHC(hcArgs, assemblyDebugOutStream, localGenotypingEngine);
                     //need to update haplotypes to find the alleles
                     EventMap.buildEventMapsForHaplotypes(context.readLikelihoods.alleles(),
                             context.assemblyResult.getFullReferenceWithPadding(),
@@ -520,6 +521,7 @@ private void filter(final CallRegionContext context) {
     }
 
     private void genotype(final CallRegionContext context) {
+        final HaplotypeCallerGenotypingEngine localGenotypingEngine = getLocalGenotypingEngine(context.region);
 
         // no need for this step?
         if ( context.regionVariants != null ) {
@@ -542,7 +544,7 @@ private void genotype(final CallRegionContext context) {
         //  haplotype containing C as reference (and vice versa).  Now this is fine if all possible haplotypes are included
         //  in the genotyping, but we lose information if we select down to a few haplotypes.  [EB]
         List<Haplotype>     haplotypes = context.readLikelihoods.alleles();
-        final CalledHaplotypes calledHaplotypes = genotypingEngine.assignGenotypeLikelihoods(
+        final CalledHaplotypes calledHaplotypes = localGenotypingEngine.assignGenotypeLikelihoods(
                 haplotypes,
                 context.readLikelihoods,
                 perSampleFilteredReadList,
@@ -582,7 +584,7 @@ private void genotype(final CallRegionContext context) {
 
                 result.addAll(referenceConfidenceModel.calculateRefConfidence(context.assemblyResult.getReferenceHaplotype(),
                         calledHaplotypes.getCalledHaplotypes(), context.assemblyResult.getPaddedReferenceLoc(), regionForGenotyping,
-                        context.readLikelihoods, genotypingEngine.getPloidyModel(), calledHaplotypes.getCalls(), hcArgs.standardArgs.genotypeArgs.supportVariants != null,
+                        context.readLikelihoods, localGenotypingEngine.getPloidyModel(), calledHaplotypes.getCalls(), hcArgs.standardArgs.genotypeArgs.supportVariants != null,
                         context.VCpriors));
 
                 context.nonVariantRightFlankRegion.ifPresent(flank -> result.addAll(referenceModelForNoVariation(flank, false, context.VCpriors)));
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 54585b1709d..4770e8536bd 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -946,6 +946,123 @@ public void testHaplotypeCallerRemoveAltAlleleBasedOnHaptypeScores() throws IOEx
         }
     }
 
+    @Test(dataProvider="HaplotypeCallerTestInputs")
+    public void testCustomPloidyRegions(final String inputFileName, final String referenceFileName) throws Exception {
+        Utils.resetRandomGenerator();
+
+        final File output = createTempFile("output", ".vcf");
+        final File expected = new File(TEST_FILES_DIR, "expected.testPloidyRegions.vcf");
+        final File ploidyRegions = new File(TEST_FILES_DIR, "testPloidyRegions.bed");
+
+        final String[] args = {
+                "-I", inputFileName,
+                "-R", referenceFileName,
+                "-L", "20:10000000-10100000",
+                "-O", output.getAbsolutePath(),
+                "-ploidy", "3",
+                "--ploidy-regions", ploidyRegions.getAbsolutePath(),
+                "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
+        };
+
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(output, expected);
+    }
+
+    // Should fail due to non-integer values in name column of bed
+    @Test(dataProvider="HaplotypeCallerTestInputs", expectedExceptions = IllegalArgumentException.class)
+    public void testNonIntegerCustomPloidyRegions(final String inputFileName, final String referenceFileName) throws Exception {
+        Utils.resetRandomGenerator();
+
+        final File output = createTempFile("output", ".vcf");
+        final File expected = new File(TEST_FILES_DIR, "expected.testPloidyRegions.vcf");
+        final File ploidyRegions = new File(TEST_FILES_DIR, "testNonIntegerPloidyRegions.bed");
+
+        final String[] args = {
+                "-I", inputFileName,
+                "-R", referenceFileName,
+                "-L", "20:10000000-10100000",
+                "-O", output.getAbsolutePath(),
+                "-ploidy", "3",
+                "--ploidy-regions", ploidyRegions.getAbsolutePath(),
+                "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
+        };
+
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(output, expected);
+    }
+
+    // Should fail due to negative integer values in name column of bed
+    @Test(dataProvider="HaplotypeCallerTestInputs", expectedExceptions = IllegalArgumentException.class)
+    public void testNonPositiveCustomPloidyRegions(final String inputFileName, final String referenceFileName) throws Exception {
+        Utils.resetRandomGenerator();
+
+        final File output = createTempFile("output", ".vcf");
+        final File expected = new File(TEST_FILES_DIR, "expected.testPloidyRegions.vcf");
+        final File ploidyRegions = new File(TEST_FILES_DIR, "testNegativePloidyRegions.bed");
+
+        final String[] args = {
+                "-I", inputFileName,
+                "-R", referenceFileName,
+                "-L", "20:10000000-10100000",
+                "-O", output.getAbsolutePath(),
+                "-ploidy", "3",
+                "--ploidy-regions", ploidyRegions.getAbsolutePath(),
+                "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
+        };
+
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(output, expected);
+    }
+
+    // Should fail due to using chr20 contig name in ploidy-regions file when BAM sequence dictionary uses 20
+    @Test(dataProvider="HaplotypeCallerTestInputs", expectedExceptions = UserException.class)
+    public void testMismatchPloidyRegionsAndSequenceDictionary(final String inputFileName, final String referenceFileName) throws Exception {
+        Utils.resetRandomGenerator();
+
+        final File output = createTempFile("output", ".vcf");
+        final File expected = new File(TEST_FILES_DIR, "expected.testPloidyRegions.vcf");
+        final File ploidyRegions = new File(TEST_FILES_DIR, "testMismatchPloidyRegions.bed");
+
+        final String[] args = {
+                "-I", inputFileName,
+                "-R", referenceFileName,
+                "-L", "20:10000000-10100000",
+                "-O", output.getAbsolutePath(),
+                "-ploidy", "3",
+                "--ploidy-regions", ploidyRegions.getAbsolutePath(),
+                "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
+        };
+
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(output, expected);
+    }
+
+    // Tests the somewhat ad hoc implementation of copying hcArgs instances in the engine, used for managing multiple ploidies used based on user inputs
+    @Test
+    public void testArgCollectionCopiesAreSynchronized() {
+        Utils.resetRandomGenerator();
+
+        HaplotypeCallerArgumentCollection hcArgs = new HaplotypeCallerArgumentCollection();
+        hcArgs.applyBQD = !hcArgs.applyBQD;
+//        hcArgs.dontGenotype = !hcArgs.dontGenotype;
+//        hcArgs.standardArgs.annotateAllSitesWithPLs = !hcArgs.standardArgs.annotateAllSitesWithPLs;
+
+        // Create copy with different ploidy and check tweaked values (and one control non-changed value) remain in sync
+        HaplotypeCallerArgumentCollection hcArgsCopy = hcArgs.copyWithNewPloidy(3);
+        Assert.assertEquals(hcArgs.applyBQD, hcArgsCopy.applyBQD);
+//        Assert.assertEquals(hcArgs.dontGenotype, hcArgsCopy.dontGenotype);
+//        Assert.assertEquals(hcArgs.standardArgs.annotateAllSitesWithPLs, hcArgsCopy.standardArgs.annotateAllSitesWithPLs);
+//        Assert.assertEquals(hcArgs.standardArgs.CONTAMINATION_FRACTION, hcArgs.standardArgs.CONTAMINATION_FRACTION);
+
+        // Modify other values of copy and check they are now distinct, i.e. a "deep copy" was created above
+//        hcArgsCopy.applyBQD = !hcArgsCopy.applyBQD;
+//        Assert.assertNotEquals(hcArgs.applyBQD, hcArgsCopy.applyBQD);
+    }
+
     // test that ReadFilterLibrary.NON_ZERO_REFERENCE_LENGTH_ALIGNMENT removes reads that consume zero reference bases
     // e.g. read name HAVCYADXX150109:1:2102:20528:2129 with cigar 23S53I
     @Test
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testPloidyRegions.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testPloidyRegions.vcf
new file mode 100644
index 00000000000..9beffa772ce
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testPloidyRegions.vcf
@@ -0,0 +1,273 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##contig=<ID=20,length=63025520>
+##contig=<ID=21,length=48129895>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+20	10000117	.	C	T	926.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.136;DP=66;ExcessHet=0.0000;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=0.913;QD=14.48;ReadPosRankSum=-0.223;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
+20	10000211	.	C	T	962.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.867;DP=54;ExcessHet=0.0000;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.057;QD=18.16;ReadPosRankSum=0.703;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906
+20	10000439	.	T	G	2819.06	.	AC=2;AF=1.00;AN=2;DP=82;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.86;QD=25.36;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,80:80:99:2833,240,0
+20	10000598	.	T	A	1956.06	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.45;QD=28.73;SOR=1.225	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1970,147,0
+20	10000694	.	G	A	1029.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.599;DP=87;ExcessHet=0.0000;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.86;MQRankSum=-5.114;QD=12.56;ReadPosRankSum=0.657;SOR=0.566	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1037,0,1601
+20	10000758	.	T	A	3853.06	.	AC=2;AF=1.00;AN=2;DP=97;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.51;QD=30.97;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3867,286,0
+20	10001019	.	T	G	671.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.541;DP=75;ExcessHet=0.0000;FS=3.406;MLEAC=1;MLEAF=0.500;MQ=47.62;MQRankSum=-7.498;QD=10.33;ReadPosRankSum=-0.925;SOR=0.665	GT:AD:DP:GQ:PL	0/1:39,26:65:99:679,0,1426
+20	10001298	.	T	A	2932.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.93;QD=27.24;SOR=0.963	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2946,220,0
+20	10001436	.	A	AAGGCT	2325.03	.	AC=2;AF=1.00;AN=2;DP=58;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.22;QD=28.20;SOR=3.014	GT:AD:DP:GQ:PL	1/1:0,52:52:99:2339,156,0
+20	10001474	.	C	T	2655.06	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.87;QD=25.00;SOR=1.516	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2669,219,0
+20	10001617	.	C	A	1752.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.261;DP=105;ExcessHet=0.0000;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.02;MQRankSum=1.373;QD=17.02;ReadPosRankSum=-0.280;SOR=1.346	GT:AD:DP:GQ:PL	0/1:52,51:103:99:1760,0,1781
+20	10001628	.	G	A	3913.06	.	AC=2;AF=1.00;AN=2;DP=98;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=29.56;SOR=1.053	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3927,285,0
+20	10001661	.	T	C	3621.06	.	AC=2;AF=1.00;AN=2;DP=85;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.13;QD=30.62;SOR=1.112	GT:AD:DP:GQ:PL	1/1:0,83:83:99:3635,249,0
+20	10001670	.	T	G	3688.06	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.60;QD=28.17;SOR=0.897	GT:AD:DP:GQ:PL	1/1:0,84:84:99:3702,253,0
+20	10002058	.	T	G	2978.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.931;DP=79;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.87;MQRankSum=3.068;QD=26.80;ReadPosRankSum=0.624;SOR=0.776	GT:AD:DP:GQ:PL	1/1:1,74:75:99:2992,216,0
+20	10002099	.	C	T	1215.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=68;ExcessHet=0.0000;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.46;MQRankSum=-0.850;QD=18.70;ReadPosRankSum=0.173;SOR=0.375	GT:AD:DP:GQ:PL	0/1:27,38:65:99:1223,0,844
+20	10002138	.	C	G	2458.06	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.64;QD=26.00;SOR=0.765	GT:AD:DP:GQ:PL	1/1:0,56:56:99:2472,169,0
+20	10002142	.	G	C	2422.06	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.08;QD=30.02;SOR=0.804	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2436,166,0
+20	10002458	.	G	GTTT	2154.96	.	AC=2;AF=1.00;AN=2;DP=65;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.67;QD=31.98;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,56:56:99:2090,167,0
+20	10002470	.	C	T	2537.06	.	AC=2;AF=1.00;AN=2;DP=68;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.92;QD=27.51;SOR=0.859	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2551,189,0
+20	10002625	.	G	T	2680.06	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.08;QD=29.11;SOR=1.127	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2694,193,0
+20	10003021	.	C	T	2398.06	.	AC=2;AF=1.00;AN=2;DP=63;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=28.08;SOR=1.071	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2412,181,0
+20	10003358	.	A	C	1475.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.004;DP=91;ExcessHet=0.0000;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.80;MQRankSum=1.011;QD=16.58;ReadPosRankSum=-1.355;SOR=0.572	GT:AD:DP:GQ:PL	0/1:45,44:89:99:1483,0,1477
+20	10003651	.	T	C	3635.06	.	AC=2;AF=1.00;AN=2;DP=98;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.24;QD=23.23;SOR=1.511	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3649,279,0
+20	10003692	.	A	G	2624.06	.	AC=2;AF=1.00;AN=2;DP=72;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=29.03;SOR=1.352	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2638,205,0
+20	10003832	.	G	A	2720.06	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.82;QD=30.67;SOR=1.473	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2734,199,0
+20	10004094	.	A	C	1840.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.62;QD=34.72;SOR=1.524	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1854,157,0
+20	10004147	.	A	G	1852.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.19;QD=26.61;SOR=1.136	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1866,156,0
+20	10004193	.	G	T	937.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.392;DP=54;ExcessHet=0.0000;FS=2.369;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=3.385;QD=18.39;ReadPosRankSum=1.724;SOR=0.941	GT:AD:DP:GQ:PL	0/1:23,28:51:99:945,0,776
+20	10004222	.	C	CA	42.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;DP=69;ExcessHet=0.0000;FS=3.221;MLEAC=1;MLEAF=0.500;MQ=58.21;MQRankSum=-2.220;QD=0.95;ReadPosRankSum=0.198;SOR=0.932	GT:AD:DP:GQ:PL	0/1:35,10:45:50:50,0,923
+20	10004223	.	A	AG	77.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=69;ExcessHet=0.0000;FS=1.242;MLEAC=1;MLEAF=0.500;MQ=58.30;MQRankSum=2.260;QD=1.62;ReadPosRankSum=0.060;SOR=0.504	GT:AD:DP:GQ:PL	0/1:36,12:48:85:85,0,983
+20	10004351	.	C	G	2770.06	.	AC=2;AF=1.00;AN=2;DP=71;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=29.20;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2784,211,0
+20	10004389	.	T	G	2509.06	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.62;QD=28.55;SOR=1.143	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2523,187,0
+20	10004610	.	A	C	3640.06	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.75;QD=34.42;SOR=0.761	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3654,267,0
+20	10004725	.	A	G	972.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.154;DP=67;ExcessHet=0.0000;FS=15.830;MLEAC=1;MLEAF=0.500;MQ=55.04;MQRankSum=3.008;QD=14.96;ReadPosRankSum=2.087;SOR=0.605	GT:AD:DP:GQ:PL	0/1:35,30:65:99:980,0,1168
+20	10004769	.	TAAAACTATGC	T	1011.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=80;ExcessHet=0.0000;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.80;MQRankSum=-6.625;QD=15.81;ReadPosRankSum=1.879;SOR=1.306	GT:AD:DP:GQ:PL	0/1:37,27:64:99:1019,0,1471
+20	10004874	.	A	C	3617.06	.	AC=2;AF=1.00;AN=2;DP=90;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=28.53;SOR=1.286	GT:AD:DP:GQ:PL	1/1:0,87:87:99:3631,261,0
+20	10004887	.	A	G	1344.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=90;ExcessHet=0.0000;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=-0.067;QD=15.82;ReadPosRankSum=-1.114;SOR=0.984	GT:AD:DP:GQ:PL	0/1:45,40:85:99:1352,0,1542
+20	10005010	.	C	T	2949.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=27.23;SOR=1.226	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2963,217,0
+20	10005427	.	C	T	2229.06	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=29.52;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2243,165,0
+20	10005499	.	A	G	3068.06	.	AC=2;AF=1.00;AN=2;DP=78;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.47;SOR=1.121	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3082,229,0
+20	10005587	.	A	G	1250.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.834;DP=76;ExcessHet=0.0000;FS=1.955;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-0.972;QD=17.37;ReadPosRankSum=0.248;SOR=0.848	GT:AD:DP:GQ:PL	0/1:36,36:72:99:1258,0,1236
+20	10005723	.	A	G	3077.06	.	AC=2;AF=1.00;AN=2;DP=88;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.79;QD=32.91;SOR=0.947	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3091,258,0
+20	10006291	.	G	A	999.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=85;ExcessHet=0.0000;FS=0.853;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-1.081;QD=11.90;ReadPosRankSum=-1.447;SOR=0.659	GT:AD:DP:GQ:PL	0/1:53,31:84:99:1007,0,1905
+20	10006404	.	A	C	2943.06	.	AC=2;AF=1.00;AN=2;DP=83;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.22;QD=31.31;SOR=1.432	GT:AD:DP:GQ:PL	1/1:0,76:76:99:2957,228,0
+20	10006682	.	T	A	2889.06	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.44;QD=31.45;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2903,219,0
+20	10006819	.	AAAAC	A	2554.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.06;QD=33.27;SOR=0.762	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2568,176,0
+20	10007150	.	G	C	690.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.476;DP=64;ExcessHet=0.0000;FS=5.048;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.96;ReadPosRankSum=-0.077;SOR=0.746	GT:AD:DP:GQ:PL	0/1:38,25:63:99:698,0,1479
+20	10007175	.	C	T	1371.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.249;DP=63;ExcessHet=0.0000;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.63;MQRankSum=1.319;QD=22.49;ReadPosRankSum=-1.213;SOR=0.434	GT:AD:DP:GQ:PL	0/1:23,38:61:99:1379,0,780
+20	10007352	.	C	T	2779.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=31.26;SOR=1.054	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2793,208,0
+20	10007531	.	A	G	2935.06	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.75;QD=27.76;SOR=1.577	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2949,217,0
+20	10007980	.	A	C	3539.06	.	AC=2;AF=1.00;AN=2;DP=92;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.70;QD=29.09;SOR=0.990	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3553,270,0
+20	10008029	.	T	TA	2010.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.409;DP=97;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.11;MQRankSum=0.651;QD=26.10;ReadPosRankSum=-1.357;SOR=0.774	GT:AD:DP:GQ:PL	1/1:3,74:77:99:2024,145,0
+20	10008146	.	TA	T	2165.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.56;QD=30.93;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2179,211,0
+20	10008221	.	T	C	3239.06	.	AC=2;AF=1.00;AN=2;DP=83;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=26.08;SOR=0.850	GT:AD:DP:GQ:PL	1/1:0,80:80:99:3253,240,0
+20	10008458	.	T	G	2669.06	.	AC=2;AF=1.00;AN=2;DP=72;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.76;QD=33.85;SOR=0.980	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2683,207,0
+20	10008742	.	G	T	736.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.893;DP=50;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.07;MQRankSum=-1.502;QD=15.03;ReadPosRankSum=0.200;SOR=0.741	GT:AD:DP:GQ:PL	0/1:23,26:49:99:744,0,580
+20	10008758	.	C	CA	707.49	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;DP=51;ExcessHet=0.0000;FS=2.191;MLEAC=1;MLEAF=0.500;MQ=37.72;MQRankSum=-0.875;QD=18.62;ReadPosRankSum=-0.262;SOR=0.405	GT:AD:DP:GQ:PL	1/1:4,34:38:10:721,10,0
+20	10008921	.	C	CA	283.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=60;ExcessHet=0.0000;FS=1.311;MLEAC=1;MLEAF=0.500;MQ=56.00;MQRankSum=-1.306;QD=8.10;ReadPosRankSum=-0.017;SOR=0.644	GT:AD:DP:GQ:PL	0/1:18,17:35:99:291,0,366
+20	10008948	.	TA	T	2091.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=56;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.26;MQRankSum=1.946;QD=27.08;ReadPosRankSum=0.884;SOR=0.721	GT:AD:DP:GQ:PL	1/1:1,53:54:99:2105,117,0
+20	10008952	.	CACACACACACA	C,CCACACACACA	1700.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=63;ExcessHet=0.0000;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.23;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.868;SOR=1.112	GT:AD:DP:GQ:PL	1/2:1,17,18:36:99:1717,539,803,595,0,533
+20	10009227	.	A	G	1390.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220;DP=63;ExcessHet=0.0000;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=56.82;MQRankSum=1.428;QD=22.43;ReadPosRankSum=-1.159;SOR=0.281	GT:AD:DP:GQ:PL	0/1:23,39:62:99:1398,0,740
+20	10009246	.	A	G	3017.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.68;QD=27.65;SOR=0.887	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3031,231,0
+20	10009400	.	T	A	3013.06	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;SOR=0.804	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3027,223,0
+20	10009512	.	C	G	3054.06	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.53;QD=30.56;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3068,231,0
+20	10009719	.	A	G	1901.06	.	AC=2;AF=1.00;AN=2;DP=65;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.71;QD=33.35;SOR=1.047	GT:AD:DP:GQ:PL	1/1:0,57:57:99:1915,170,0
+20	10009795	.	A	G	1895.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=33.63;SOR=1.514	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1909,141,0
+20	10009842	.	G	GAA	562.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=52;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.936;QD=16.07;ReadPosRankSum=1.757;SOR=0.602	GT:AD:DP:GQ:PL	0/1:19,16:35:99:570,0,691
+20	10009844	.	G	A	683.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.116;DP=54;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.61;MQRankSum=0.975;QD=19.53;ReadPosRankSum=-2.419;SOR=0.793	GT:AD:DP:GQ:PL	0/1:16,19:35:99:691,0,585
+20	10009871	.	A	G	679.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=62;ExcessHet=0.0000;FS=1.273;MLEAC=1;MLEAF=0.500;MQ=51.11;MQRankSum=1.336;QD=18.37;ReadPosRankSum=0.840;SOR=0.631	GT:AD:DP:GQ:PL	0/1:18,19:37:99:687,0,593
+20	10009875	.	A	G,AGGGAGG	2389.06	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.378;DP=58;ExcessHet=0.0000;FS=6.463;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.413;QD=30.55;ReadPosRankSum=1.373;SOR=0.461	GT:AD:DP:GQ:PL	1/2:2,15,14:31:99:2406,645,532,697,0,574
+20	10009879	.	A	G	2259.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.534;DP=53;ExcessHet=0.0000;FS=8.605;MLEAC=2;MLEAF=1.00;MQ=50.48;MQRankSum=1.681;QD=32.62;ReadPosRankSum=1.113;SOR=1.198	GT:AD:DP:GQ:PL	1/1:2,51:53:99:2273,150,0
+20	10009883	.	A	G	2166.06	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.81;QD=29.33;SOR=1.755	GT:AD:DP:GQ:PL	1/1:0,49:49:99:2180,147,0
+20	10010393	.	T	G	1473.99	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-3.351;DP=79;FS=11.600;MLEAC=2;MLEAF=0.667;MQ=59.42;MQRankSum=-1.284;QD=18.66;ReadPosRankSum=-1.738;SOR=0.606	GT:AD:DP:GQ:PL	0/1/1:36,43:79:22:1484,22,0,1221
+20	10010536	.	G	GA	2453.32	.	AC=3;AF=1.00;AN=3;DP=92;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=61.74;QD=30.67;SOR=0.850	GT:AD:DP:GQ:PL	1/1/1:0,80:80:99:2469,381,141,0
+20	10010766	.	T	G	2424.36	.	AC=3;AF=1.00;AN=3;DP=70;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=60.00;QD=35.36;SOR=0.818	GT:AD:DP:GQ:PL	1/1/1:0,66:66:99:2440,315,116,0
+20	10010832	.	T	C	2964.36	.	AC=3;AF=1.00;AN=3;DP=76;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.51;QD=34.30;SOR=1.091	GT:AD:DP:GQ:PL	1/1/1:0,75:75:99:2980,358,132,0
+20	10011075	.	C	T	1334.05	.	AC=1;AF=0.333;AN=3;BaseQRankSum=5.364;DP=86;FS=1.800;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=16.07;ReadPosRankSum=-1.036;SOR=0.968	GT:AD:DP:GQ:PL	0/0/1:44,39:83:14:1340,0,14,1319
+20	10011309	.	T	C	2705.36	.	AC=3;AF=1.00;AN=3;DP=80;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=60.00;QD=27.00;SOR=1.223	GT:AD:DP:GQ:PL	1/1/1:0,77:77:99:2721,366,135,0
+20	10011517	.	GA	G	526	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.924;DP=99;FS=2.130;MLEAC=1;MLEAF=0.333;MQ=59.91;MQRankSum=2.041;QD=6.92;ReadPosRankSum=0.603;SOR=0.412	GT:AD:DP:GQ:PL	0/0/1:46,30:76:46:532,0,46,880
+20	10011666	.	C	T	2974.36	.	AC=3;AF=1.00;AN=3;DP=74;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.06;QD=30.82;SOR=1.103	GT:AD:DP:GQ:PL	1/1/1:0,73:73:99:2990,348,129,0
+20	10011939	.	C	T	2526.36	.	AC=3;AF=1.00;AN=3;DP=66;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=56.55;QD=29.27;SOR=1.329	GT:AD:DP:GQ:PL	1/1/1:0,62:62:99:2542,296,109,0
+20	10012021	.	CA	C	1998.32	.	AC=3;AF=1.00;AN=3;DP=71;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=57.12;QD=30.28;SOR=1.196	GT:AD:DP:GQ:PL	1/1/1:0,66:66:99:2014,314,116,0
+20	10012362	.	G	T	848.36	.	AC=3;AF=1.00;AN=3;DP=25;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=54.31;QD=35.92;SOR=4.003	GT:AD:DP:GQ:PL	1/1/1:0,23:23:40:864,109,40,0
+20	10012384	.	T	C	250.21	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.773;DP=18;FS=7.375;MLEAC=1;MLEAF=0.333;MQ=53.38;MQRankSum=-0.811;QD=13.90;ReadPosRankSum=0.800;SOR=0.044	GT:AD:DP:GQ:PL	0/0/1:10,8:18:6:256,0,6,353
+20	10012387	.	T	C	546.34	.	AC=3;AF=1.00;AN=3;DP=18;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=53.38;QD=32.14;SOR=3.383	GT:AD:DP:GQ:PL	1/1/1:0,17:17:29:562,78,29,0
+20	10012479	.	A	G	587.34	.	AC=3;AF=1.00;AN=3;DP=18;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=51.29;QD=34.55;SOR=0.804	GT:AD:DP:GQ:PL	1/1/1:0,17:17:29:603,79,29,0
+20	10012498	.	C	G	434.23	.	AC=3;AF=1.00;AN=3;DP=10;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=43.25;QD=29.63;SOR=1.609	GT:AD:DP:GQ:PL	1/1/1:0,10:10:18:450,48,18,0
+20	10012518	.	T	C	464.25	.	AC=3;AF=1.00;AN=3;DP=12;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=43.58;QD=28.76;SOR=1.270	GT:AD:DP:GQ:PL	1/1/1:0,11:11:19:480,52,19,0
+20	10012521	.	C	T	97.07	.	AC=1;AF=0.333;AN=3;BaseQRankSum=1.517;DP=12;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=40.86;MQRankSum=-0.376;QD=8.09;ReadPosRankSum=2.405;SOR=0.693	GT:AD:DP:GQ:PL	0/0/1:8,4:12:12:103,0,12,224
+20	10012570	.	G	GCA	479.21	.	AC=3;AF=1.00;AN=3;DP=11;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=39.52;QD=29.94;SOR=3.442	GT:AD:DP:GQ:PL	1/1/1:0,11:11:19:495,52,19,0
+20	10012572	.	GT	G	479.21	.	AC=3;AF=1.00;AN=3;DP=12;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=40.60;QD=31.54;SOR=3.442	GT:AD:DP:GQ:PL	1/1/1:0,11:11:19:495,52,19,0
+20	10012631	.	C	CG	513.88	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-1.030;DP=21;FS=8.822;MLEAC=2;MLEAF=0.667;MQ=48.34;MQRankSum=-1.670;QD=24.47;ReadPosRankSum=-1.777;SOR=0.048	GT:AD:DP:GQ:PL	0/1/1:8,13:21:15:524,15,0,299
+20	10012636	.	G	C	548.97	.	AC=2;AF=0.667;AN=3;BaseQRankSum=2.711;DP=22;FS=5.959;MLEAC=2;MLEAF=0.667;MQ=48.93;MQRankSum=-1.513;QD=24.95;ReadPosRankSum=-1.777;SOR=0.058	GT:AD:DP:GQ:PL	0/1/1:8,14:22:18:559,18,0,297
+20	10012714	.	G	C	1313.36	.	AC=3;AF=1.00;AN=3;DP=36;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=52.52;QD=28.86;SOR=2.964	GT:AD:DP:GQ:PL	1/1/1:0,35:35:62:1329,167,62,0
+20	10012751	.	T	C	950.36	.	AC=3;AF=1.00;AN=3;DP=31;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=50.73;QD=31.68;SOR=0.976	GT:AD:DP:GQ:PL	1/1/1:0,30:30:52:966,140,52,0
+20	10013119	.	C	T	1018.56	.	AC=2;AF=0.667;AN=3;BaseQRankSum=2.724;DP=61;FS=2.248;MLEAC=1;MLEAF=0.333;MQ=51.43;MQRankSum=-1.089;QD=17.26;ReadPosRankSum=0.159;SOR=0.405	GT:AD:DP:GQ:PL	0/1/1:29,30:59:3:1026,3,0,922
+20	10013574	.	G	A	1066.03	.	AC=1;AF=0.333;AN=3;BaseQRankSum=3.469;DP=73;FS=7.109;MLEAC=1;MLEAF=0.333;MQ=58.17;MQRankSum=-0.271;QD=15.45;ReadPosRankSum=0.706;SOR=1.675	GT:AD:DP:GQ:PL	0/0/1:38,31:69:21:1072,0,21,1294
+20	10014990	.	C	CAT	1249.52	.	AC=2;AF=0.667;AN=3;BaseQRankSum=1.930;DP=89;FS=2.076;MLEAC=1;MLEAF=0.333;MQ=60.88;MQRankSum=3.260;QD=16.23;ReadPosRankSum=-0.311;SOR=0.429	GT:AD:DP:GQ:PL	0/1/1:38,39:77:3:1257,3,0,1229
+20	10015679	.	C	T	160.79	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.200;DP=10;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=16.08;ReadPosRankSum=0.497;SOR=0.693	GT:AD:DP:GQ:PL	0/0/1:5,5:10:0:166,0,0,163
+20	10015761	.	T	C	362.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-1.982;DP=23;FS=0.000;MLEAC=2;MLEAF=0.667;MQ=58.99;MQRankSum=1.294;QD=16.50;ReadPosRankSum=1.805;SOR=0.352	GT:AD:DP:GQ:PL	0/1/1:9,13:22:11:373,11,0,284
+20	10018158	.	G	C	1646.99	.	AC=2;AF=0.667;AN=3;BaseQRankSum=5.213;DP=94;FS=0.808;MLEAC=2;MLEAF=0.667;MQ=59.80;MQRankSum=1.118;QD=18.72;ReadPosRankSum=1.179;SOR=0.834	GT:AD:DP:GQ:PL	0/1/1:40,48:88:24:1657,24,0,1154
+20	10018555	.	G	A	1581	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-0.627;DP=84;FS=4.241;MLEAC=2;MLEAF=0.667;MQ=60.00;MQRankSum=0.000;QD=19.76;ReadPosRankSum=0.815;SOR=0.627	GT:AD:DP:GQ:PL	0/1/1:35,45:80:30:1591,30,0,1206
+20	10019093	.	A	G	1250.05	.	AC=2;AF=0.667;AN=3;BaseQRankSum=0.452;DP=73;FS=1.990;MLEAC=2;MLEAF=0.667;MQ=59.68;MQRankSum=1.073;QD=18.12;ReadPosRankSum=-0.252;SOR=0.665	GT:AD:DP:GQ:PL	0/1/1:33,36:69:10:1260,10,0,1091
+20	10020229	.	G	A	1559.26	.	AC=2;AF=0.500;AN=4;BaseQRankSum=5.792;DP=84;FS=0.833;MLEAC=2;MLEAF=0.500;MQ=59.50;MQRankSum=0.104;QD=19.02;ReadPosRankSum=-0.549;SOR=0.573	GT:AD:DP:GQ:PL	0/0/1/1:38,44:82:37:1567,66,0,37,1130
+20	10023689	.	G	A	1874.21	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.144;DP=82;FS=0.877;MLEAC=2;MLEAF=0.500;MQ=59.77;MQRankSum=1.352;QD=23.43;ReadPosRankSum=1.162;SOR=0.549	GT:AD:DP:GQ:PL	0/1/1/1:29,51:80:3:1883,105,3,0,948
+20	10024107	.	C	T	1715.26	.	AC=2;AF=0.500;AN=4;BaseQRankSum=5.770;DP=89;FS=0.817;MLEAC=2;MLEAF=0.500;MQ=59.43;MQRankSum=-1.546;QD=19.94;ReadPosRankSum=0.148;SOR=0.823	GT:AD:DP:GQ:PL	0/0/1/1:38,48:86:29:1723,78,0,29,1086
+20	10024300	.	CTT	C,CTTTT	191.75	.	AC=1,2;AF=0.250,0.500;AN=4;BaseQRankSum=1.975;DP=53;FS=2.963;MLEAC=1,1;MLEAF=0.250,0.250;MQ=52.89;MQRankSum=-1.143;QD=13.70;ReadPosRankSum=-0.297;SOR=1.981	GT:AD:DP:GQ:PL	0/1/2/2:2,4,8:14:12:198,123,140,182,447,100,12,19,80,92,0,46,101,38,202
+20	10026357	.	T	C	1187.27	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-1.700;DP=63;FS=8.911;MLEAC=2;MLEAF=0.500;MQ=58.43;MQRankSum=-0.148;QD=18.85;ReadPosRankSum=-0.076;SOR=0.722	GT:AD:DP:GQ:PL	0/0/1/1:28,35:63:23:1195,56,0,23,932
+20	10026794	.	C	T	1107.28	.	AC=2;AF=0.500;AN=4;BaseQRankSum=2.828;DP=56;FS=2.399;MLEAC=2;MLEAF=0.500;MQ=59.59;MQRankSum=-0.719;QD=21.29;ReadPosRankSum=-0.533;SOR=0.428	GT:AD:DP:GQ:PL	0/0/1/1:19,33:52:0:1114,65,0,0,529
+20	10027234	.	A	ATTAG	1350.22	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-0.406;DP=75;FS=3.248;MLEAC=2;MLEAF=0.500;MQ=57.44;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.510;SOR=0.926	GT:AD:DP:GQ:PL	0/0/1/1:34,35:69:41:1358,45,0,41,1320
+20	10027868	.	A	G	1760.26	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-5.793;DP=91;FS=6.873;MLEAC=2;MLEAF=0.500;MQ=59.49;MQRankSum=0.047;QD=19.56;ReadPosRankSum=1.872;SOR=0.937	GT:AD:DP:GQ:PL	0/0/1/1:44,46:90:51:1768,61,0,51,1671
+20	10027872	.	A	G	1745.26	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-5.491;DP=88;FS=8.704;MLEAC=2;MLEAF=0.500;MQ=59.48;MQRankSum=0.065;QD=20.06;ReadPosRankSum=1.053;SOR=0.834	GT:AD:DP:GQ:PL	0/0/1/1:42,45:87:47:1753,61,0,47,1606
+20	10028867	.	A	ATG	1137.23	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-0.874;DP=93;FS=4.652;MLEAC=2;MLEAF=0.500;MQ=60.68;MQRankSum=2.711;QD=16.02;ReadPosRankSum=0.630;SOR=0.336	GT:AD:DP:GQ:PL	0/0/1/1:32,39:71:28:1145,60,0,28,915
+20	10030188	.	T	A	1378.12	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.711;DP=82;FS=9.186;MLEAC=1;MLEAF=0.333;MQ=59.49;MQRankSum=-1.013;QD=17.01;ReadPosRankSum=-0.553;SOR=1.105	GT:AD:DP:GQ:PL	0/0/1:42,39:81:9:1384,0,9,1508
+20	10031254	.	A	AT	1482.96	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-0.091;DP=90;FS=9.250;MLEAC=2;MLEAF=0.667;MQ=59.91;MQRankSum=0.017;QD=17.45;ReadPosRankSum=0.663;SOR=0.211	GT:AD:DP:GQ:PL	0/1/1:38,47:85:27:1493,27,0,1151
+20	10031342	.	G	A	1846.01	.	AC=2;AF=0.667;AN=3;BaseQRankSum=1.833;DP=93;FS=1.714;MLEAC=2;MLEAF=0.667;MQ=59.75;MQRankSum=-0.866;QD=19.85;ReadPosRankSum=-0.012;SOR=0.955	GT:AD:DP:GQ:PL	0/1/1:41,52:93:33:1856,33,0,1367
+20	10031798	.	G	A	4309.36	.	AC=3;AF=1.00;AN=3;DP=107;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.61;QD=29.41;SOR=0.900	GT:AD:DP:GQ:PL	1/1/1:0,104:104:99:4325,496,183,0
+20	10031827	.	C	T	2000.94	.	AC=2;AF=0.667;AN=3;BaseQRankSum=3.552;DP=115;FS=4.729;MLEAC=2;MLEAF=0.667;MQ=59.84;MQRankSum=-0.945;QD=18.53;ReadPosRankSum=-1.396;SOR=0.382	GT:AD:DP:GQ:PL	0/1/1:52,56:108:12:2011,12,0,1776
+20	10032094	.	G	A	1238.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=5.488;DP=86;FS=6.039;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=14.92;ReadPosRankSum=-0.579;SOR=0.260	GT:AD:DP:GQ:PL	0/0/1:47,36:83:32:1244,0,32,1492
+20	10032413	.	T	G	881.07	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-6.142;DP=66;FS=10.444;MLEAC=1;MLEAF=0.333;MQ=59.43;MQRankSum=-0.065;QD=13.35;ReadPosRankSum=-1.003;SOR=1.293	GT:AD:DP:GQ:PL	0/0/1:35,31:66:12:887,0,12,1266
+20	10032882	.	A	T	1210.12	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-3.697;DP=76;FS=4.673;MLEAC=1;MLEAF=0.333;MQ=59.70;MQRankSum=-1.014;QD=16.13;ReadPosRankSum=0.626;SOR=0.338	GT:AD:DP:GQ:PL	0/0/1:39,36:75:9:1216,0,9,1391
+20	10032972	.	C	CAT	1143.08	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.354;DP=67;FS=5.062;MLEAC=1;MLEAF=0.333;MQ=59.66;MQRankSum=-1.017;QD=18.14;ReadPosRankSum=-0.723;SOR=1.300	GT:AD:DP:GQ:PL	0/0/1:33,30:63:9:1149,0,9,1284
+20	10034306	.	T	C	812.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-3.661;DP=80;FS=0.890;MLEAC=1;MLEAF=0.333;MQ=59.48;MQRankSum=1.150;QD=10.83;ReadPosRankSum=0.539;SOR=0.685	GT:AD:DP:GQ:PL	0/0/1:46,29:75:52:818,0,52,1600
+20	10036930	.	CGATAGCCCTAGCCCTAGATA	C	1060.99	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.720;DP=98;FS=11.152;MLEAC=1;MLEAF=0.333;MQ=54.46;MQRankSum=-4.048;QD=15.60;ReadPosRankSum=0.460;SOR=0.269	GT:AD:DP:GQ:PL	0/0/1:39,29:68:26:1067,0,26,1503
+20	10037037	.	C	T	1439.94	.	AC=2;AF=0.667;AN=3;BaseQRankSum=3.504;DP=88;FS=1.943;MLEAC=2;MLEAF=0.667;MQ=60.08;MQRankSum=-1.193;QD=17.78;ReadPosRankSum=-1.609;SOR=0.495	GT:AD:DP:GQ:PL	0/1/1:39,42:81:12:1450,12,0,1110
+20	10037110	.	T	TGATA	2802.32	.	AC=3;AF=1.00;AN=3;DP=84;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=55.01;QD=31.11;SOR=0.933	GT:AD:DP:GQ:PL	1/1/1:0,63:63:99:2818,300,110,0
+20	10037144	.	T	TGATAGATA	1845.32	.	AC=3;AF=1.00;AN=3;DP=81;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=53.21;QD=34.66;SOR=1.179	GT:AD:DP:GQ:PL	1/1/1:0,43:43:74:1861,202,74,0
+20	10037709	.	A	T	1019.03	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-2.367;DP=73;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=59.68;MQRankSum=0.934;QD=14.35;ReadPosRankSum=0.040;SOR=0.608	GT:AD:DP:GQ:PL	0/0/1:39,32:71:22:1025,0,22,1347
+20	10039371	.	T	G	1332.97	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-3.260;DP=76;FS=6.144;MLEAC=2;MLEAF=0.667;MQ=60.00;MQRankSum=0.000;QD=18.01;ReadPosRankSum=0.391;SOR=1.031	GT:AD:DP:GQ:PL	0/1/1:34,40:74:18:1343,18,0,1184
+20	10040772	.	C	CT	2018.32	.	AC=3;AF=1.00;AN=3;DP=85;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=52.32;QD=28.83;SOR=0.811	GT:AD:DP:GQ:PL	1/1/1:0,70:70:99:2034,333,123,0
+20	10040812	.	AT	A	2629.32	.	AC=3;AF=1.00;AN=3;DP=83;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=51.21;QD=29.40;SOR=0.721	GT:AD:DP:GQ:PL	1/1/1:0,71:71:99:2645,339,125,0
+20	10040821	.	T	A	1174.63	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-0.021;DP=84;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=51.33;MQRankSum=-0.097;QD=15.06;ReadPosRankSum=-1.350;SOR=0.688	GT:AD:DP:GQ:PL	0/1/1:38,40:78:7:1184,7,0,1083
+20	10041304	.	C	T	2778.36	.	AC=3;AF=1.00;AN=3;DP=68;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.39;QD=36.76;SOR=0.693	GT:AD:DP:GQ:PL	1/1/1:0,68:68:99:2794,324,119,0
+20	10041698	.	C	CAT	60.98	.	AC=1;AF=0.333;AN=3;BaseQRankSum=1.887;DP=80;FS=1.616;MLEAC=1;MLEAF=0.333;MQ=58.63;MQRankSum=0.194;QD=1.07;ReadPosRankSum=-0.164;SOR=1.148	GT:AD:DP:GQ:PL	0/0/1:50,7:57:67:67,0,129,1477
+20	10041701	.	A	ATATG	1478.97	.	AC=2;AF=0.667;AN=3;BaseQRankSum=0.848;DP=80;FS=3.477;MLEAC=2;MLEAF=0.667;MQ=58.93;MQRankSum=0.340;QD=25.07;ReadPosRankSum=-0.023;SOR=0.260	GT:AD:DP:GQ:PL	0/1/1:9,50:59:99:1489,124,0,104
+20	10042319	.	C	T	2671.36	.	AC=3;AF=1.00;AN=3;DP=69;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.06;QD=30.54;SOR=1.033	GT:AD:DP:GQ:PL	1/1/1:0,66:66:99:2687,315,116,0
+20	10042761	.	A	G	3566.36	.	AC=3;AF=1.00;AN=3;DP=94;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=60.00;QD=21.53;SOR=1.389	GT:AD:DP:GQ:PL	1/1/1:0,91:91:99:3582,431,159,0
+20	10042829	.	A	G	3068.36	.	AC=3;AF=1.00;AN=3;DP=82;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.77;QD=34.87;SOR=0.855	GT:AD:DP:GQ:PL	1/1/1:0,78:78:99:3084,372,137,0
+20	10043002	.	A	T	1303.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=3.986;DP=89;FS=2.877;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=15.15;ReadPosRankSum=-0.035;SOR=0.434	GT:AD:DP:GQ:PL	0/0/1:48,38:86:30:1309,0,30,1651
+20	10044849	.	A	G	2104.36	.	AC=3;AF=1.00;AN=3;DP=59;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.61;QD=31.04;SOR=1.316	GT:AD:DP:GQ:PL	1/1/1:0,59:59:99:2120,280,103,0
+20	10045078	.	G	T	3284.36	.	AC=3;AF=1.00;AN=3;DP=84;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=58.78;QD=27.86;SOR=0.876	GT:AD:DP:GQ:PL	1/1/1:0,81:81:99:3300,386,143,0
+20	10045642	.	G	C	3120.36	.	AC=3;AF=1.00;AN=3;DP=82;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.49;QD=34.17;SOR=0.821	GT:AD:DP:GQ:PL	1/1/1:0,81:81:99:3136,385,142,0
+20	10046178	.	AAGAAAGAAAG	A	2134.32	.	AC=3;AF=1.00;AN=3;DP=63;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=48.77;QD=28.60;SOR=0.818	GT:AD:DP:GQ:PL	1/1/1:0,49:49:87:2150,236,87,0
+20	10046537	.	A	G	827.56	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-3.909;DP=57;FS=3.724;MLEAC=1;MLEAF=0.333;MQ=54.50;MQRankSum=0.395;QD=14.52;ReadPosRankSum=0.727;SOR=1.262	GT:AD:DP:GQ:PL	0/1/1:28,29:57:3:835,3,0,889
+20	10050828	.	T	C	1246.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-2.704;DP=91;FS=2.887;MLEAC=1;MLEAF=0.333;MQ=59.54;MQRankSum=0.892;QD=14.49;ReadPosRankSum=-0.140;SOR=0.521	GT:AD:DP:GQ:PL	0/0/1:49,37:86:35:1252,0,35,1764
+20	10051448	.	T	C	1139.79	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.501;DP=71;FS=3.687;MLEAC=1;MLEAF=0.333;MQ=59.41;MQRankSum=-1.404;QD=16.28;ReadPosRankSum=-0.705;SOR=0.302	GT:AD:DP:GQ:PL	0/0/1:35,35:70:0:1145,0,0,1132
+20	10052688	.	C	A	1085.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.180;DP=83;FS=3.135;MLEAC=1;MLEAF=0.333;MQ=59.78;MQRankSum=0.870;QD=14.09;ReadPosRankSum=1.443;SOR=0.379	GT:AD:DP:GQ:PL	0/0/1:45,32:77:39:1091,0,39,1645
+20	10058022	.	T	C	987.06	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-2.346;DP=72;FS=0.920;MLEAC=1;MLEAF=0.333;MQ=59.16;MQRankSum=0.466;QD=14.52;ReadPosRankSum=0.018;SOR=0.849	GT:AD:DP:GQ:PL	0/0/1:36,32:68:13:993,0,13,1251
+20	10067049	.	TAAAAAAA	T	534.01	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.674;DP=73;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=54.73;MQRankSum=-0.605;QD=24.27;ReadPosRankSum=-1.645;SOR=0.892	GT:AD:DP:GQ:PL	1:2,20:22:99:544,0
+20	10067090	.	C	A	2023.04	.	AC=1;AF=1.00;AN=1;DP=56;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=54.57;QD=25.57;SOR=0.729	GT:AD:DP:GQ:PL	1:0,55:55:99:2033,0
+20	10067264	.	G	A	2941.04	.	AC=1;AF=1.00;AN=1;DP=73;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.37;QD=33.11;SOR=0.776	GT:AD:DP:GQ:PL	1:0,73:73:99:2951,0
+20	10067722	.	A	C	2165.04	.	AC=1;AF=1.00;AN=1;DP=59;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.20;SOR=0.846	GT:AD:DP:GQ:PL	1:0,54:54:99:2175,0
+20	10068158	.	GTGTATATATATA	G	38.01	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.842;DP=28;FS=3.680;MLEAC=1;MLEAF=1.00;MQ=56.62;MQRankSum=0.328;QD=5.43;ReadPosRankSum=0.524;SOR=0.061	GT:AD:DP:GQ:PL	1:3,4:7:48:48,0
+20	10068981	.	G	A	2522.04	.	AC=1;AF=1.00;AN=1;DP=65;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.49;SOR=0.941	GT:AD:DP:GQ:PL	1:0,61:61:99:2532,0
+20	10070602	.	T	C	2710.04	.	AC=1;AF=1.00;AN=1;DP=76;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=58.78;QD=31.67;SOR=0.749	GT:AD:DP:GQ:PL	1:0,72:72:99:2720,0
+20	10070936	.	T	A	3650.04	.	AC=1;AF=1.00;AN=1;DP=86;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=58.96;QD=29.53;SOR=0.846	GT:AD:DP:GQ:PL	1:0,82:82:99:3660,0
+20	10070938	.	G	GA	3684.01	.	AC=1;AF=1.00;AN=1;DP=85;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.07;QD=32.63;SOR=0.818	GT:AD:DP:GQ:PL	1:0,83:83:99:3694,0
+20	10071135	.	C	T	3276.04	.	AC=1;AF=1.00;AN=1;DP=88;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.21;QD=30.36;SOR=1.003	GT:AD:DP:GQ:PL	1:0,79:79:99:3286,0
+20	10071187	.	G	A	3429.04	.	AC=1;AF=1.00;AN=1;DP=85;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.73;QD=28.13;SOR=1.367	GT:AD:DP:GQ:PL	1:0,82:82:99:3439,0
+20	10071890	.	T	C	1993.04	.	AC=1;AF=1.00;AN=1;DP=61;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.31;QD=34.97;SOR=0.728	GT:AD:DP:GQ:PL	1:0,57:57:99:2003,0
+20	10072505	.	A	G	2118.04	.	AC=1;AF=1.00;AN=1;DP=67;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.09;SOR=0.822	GT:AD:DP:GQ:PL	1:0,64:64:99:2128,0
+20	10074187	.	A	G	3120.04	.	AC=1;AF=1.00;AN=1;DP=81;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.14;QD=27.97;SOR=0.881	GT:AD:DP:GQ:PL	1:0,79:79:99:3130,0
+20	10074240	.	T	C	3425.04	.	AC=1;AF=1.00;AN=1;DP=89;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.79;QD=28.31;SOR=0.922	GT:AD:DP:GQ:PL	1:0,85:85:99:3435,0
+20	10074716	.	G	A	2419.04	.	AC=1;AF=1.00;AN=1;DP=70;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.67;QD=35.21;SOR=1.214	GT:AD:DP:GQ:PL	1:0,64:64:99:2429,0
+20	10074806	.	G	A	2836.04	.	AC=1;AF=1.00;AN=1;DP=75;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.38;QD=35.18;SOR=0.840	GT:AD:DP:GQ:PL	1:0,71:71:99:2846,0
+20	10075043	.	T	C	2424.04	.	AC=1;AF=1.00;AN=1;DP=64;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.64;QD=29.59;SOR=1.107	GT:AD:DP:GQ:PL	1:0,61:61:99:2434,0
+20	10075168	.	C	T	3631.04	.	AC=1;AF=1.00;AN=1;DP=91;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.37;QD=32.25;SOR=0.997	GT:AD:DP:GQ:PL	1:0,88:88:99:3641,0
+20	10075508	.	GA	G	1956.01	.	AC=1;AF=1.00;AN=1;DP=81;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=61.11;QD=27.94;SOR=1.085	GT:AD:DP:GQ:PL	1:0,70:70:99:1966,0
+20	10076339	.	A	G	293.04	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.069;DP=76;FS=1.992;MLEAC=1;MLEAF=1.00;MQ=59.70;MQRankSum=-0.866;QD=4.07;ReadPosRankSum=1.015;SOR=0.446	GT:AD:DP:GQ:PL	1:32,40:72:99:303,0
+20	10076399	.	G	A	282.04	.	AC=1;AF=1.00;AN=1;BaseQRankSum=4.154;DP=95;FS=1.680;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=3.00;ReadPosRankSum=-1.058;SOR=0.952	GT:AD:DP:GQ:PL	1:44,50:94:99:292,0
+20	10077752	.	T	C	178.04	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-6.503;DP=83;FS=4.458;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=2.25;ReadPosRankSum=-0.352;SOR=1.251	GT:AD:DP:GQ:PL	1:34,45:79:99:188,0
+20	10081750	.	C	A	1362.05	.	AC=1;AF=0.333;AN=3;BaseQRankSum=2.670;DP=92;FS=0.824;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=16.41;ReadPosRankSum=-0.406;SOR=0.664	GT:AD:DP:GQ:PL	0/0/1:44,39:83:14:1368,0,14,1511
+20	10081800	.	C	T	1118.21	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.241;DP=69;FS=11.086;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=16.44;ReadPosRankSum=-2.622;SOR=0.143	GT:AD:DP:GQ:PL	0/0/1:35,33:68:6:1124,0,6,1208
+20	10082892	.	C	T	1725.36	.	AC=3;AF=1.00;AN=3;DP=45;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.49;QD=34.86;SOR=0.883	GT:AD:DP:GQ:PL	1/1/1:0,44:44:77:1741,209,77,0
+20	10085211	.	A	T	1220.07	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.501;DP=81;FS=0.870;MLEAC=1;MLEAF=0.333;MQ=59.72;MQRankSum=-1.028;QD=16.05;ReadPosRankSum=-1.405;SOR=0.723	GT:AD:DP:GQ:PL	0/0/1:40,36:76:12:1226,0,12,1429
+20	10086110	.	G	A	1284.05	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.343;DP=83;FS=1.810;MLEAC=1;MLEAF=0.333;MQ=59.16;MQRankSum=-0.680;QD=15.85;ReadPosRankSum=0.170;SOR=0.495	GT:AD:DP:GQ:PL	0/0/1:43,38:81:15:1290,0,15,1493
+20	10086283	.	G	T	1056.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=2.304;DP=86;FS=0.855;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=12.57;ReadPosRankSum=1.889;SOR=0.529	GT:AD:DP:GQ:PL	0/0/1:52,32:84:60:1062,0,60,1779
+20	10086619	.	T	A	831.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.256;DP=76;FS=0.958;MLEAC=1;MLEAF=0.333;MQ=59.70;MQRankSum=-1.312;QD=11.87;ReadPosRankSum=-0.760;SOR=0.846	GT:AD:DP:GQ:PL	0/0/1:45,25:70:60:837,0,60,1616
+20	10086853	.	G	A	1020.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=3.915;DP=75;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=59.44;MQRankSum=-0.177;QD=13.97;ReadPosRankSum=-0.100;SOR=0.767	GT:AD:DP:GQ:PL	0/0/1:41,32:73:28:1026,0,28,1276
+20	10086954	.	G	A	1101.63	.	AC=1;AF=0.333;AN=3;BaseQRankSum=2.606;DP=70;FS=4.812;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=16.20;ReadPosRankSum=-0.534;SOR=1.185	GT:AD:DP:GQ:PL	0/0/1:34,34:68:1:1107,0,1,1034
+20	10087230	.	A	G	1855.01	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-2.407;DP=101;FS=3.860;MLEAC=2;MLEAF=0.667;MQ=58.94;MQRankSum=1.707;QD=19.32;ReadPosRankSum=0.307;SOR=0.960	GT:AD:DP:GQ:PL	0/1/1:42,54:96:36:1865,36,0,1421
+20	10087394	.	T	G	1707.01	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-2.340;DP=85;FS=4.225;MLEAC=2;MLEAF=0.667;MQ=59.46;MQRankSum=1.207;QD=20.32;ReadPosRankSum=0.885;SOR=0.436	GT:AD:DP:GQ:PL	0/1/1:35,49:84:42:1717,42,0,1186
+20	10087754	.	T	G	1387.92	.	AC=2;AF=0.667;AN=3;BaseQRankSum=0.239;DP=87;FS=0.851;MLEAC=2;MLEAF=0.667;MQ=60.60;MQRankSum=2.166;QD=17.57;ReadPosRankSum=-0.378;SOR=0.596	GT:AD:DP:GQ:PL	0/1/1:37,42:79:14:1398,14,0,1223
+20	10087804	.	C	T	1617	.	AC=2;AF=0.667;AN=3;BaseQRankSum=1.940;DP=104;FS=3.847;MLEAC=1;MLEAF=0.333;MQ=60.18;MQRankSum=2.618;QD=16.17;ReadPosRankSum=0.341;SOR=0.369	GT:AD:DP:GQ:PL	0/1/1:50,50:100:1:1623,1,0,1486
+20	10087820	.	C	CAG	474.98	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.974;DP=103;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=60.51;MQRankSum=0.422;QD=8.64;ReadPosRankSum=-0.019;SOR=0.850	GT:AD:DP:GQ:PL	0/0/1:37,18:55:59:481,0,59,1184
+20	10088063	.	C	T	1423.06	.	AC=1;AF=0.333;AN=3;BaseQRankSum=3.405;DP=94;FS=2.739;MLEAC=1;MLEAF=0.333;MQ=59.36;MQRankSum=0.515;QD=15.30;ReadPosRankSum=0.285;SOR=1.053	GT:AD:DP:GQ:PL	0/0/1:49,44:93:13:1429,0,13,1386
+20	10088699	.	C	T	798.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=3.803;DP=67;FS=16.952;MLEAC=1;MLEAF=0.333;MQ=56.90;MQRankSum=-3.140;QD=12.87;ReadPosRankSum=-1.456;SOR=1.914	GT:AD:DP:GQ:PL	0/0/1:36,26:62:30:804,0,30,1087
+20	10088730	.	G	A	987.07	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.224;DP=57;FS=9.708;MLEAC=1;MLEAF=0.333;MQ=52.92;MQRankSum=-5.213;QD=17.63;ReadPosRankSum=0.581;SOR=1.011	GT:AD:DP:GQ:PL	0/0/1:30,26:56:12:993,0,12,1144
+20	10088736	.	A	C	1092.21	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.282;DP=60;FS=7.080;MLEAC=1;MLEAF=0.333;MQ=52.86;MQRankSum=-5.157;QD=18.20;ReadPosRankSum=0.573;SOR=0.850	GT:AD:DP:GQ:PL	0/0/1:31,29:60:6:1098,0,6,1181
+20	10088747	.	A	G	1121.94	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-3.877;DP=56;FS=9.708;MLEAC=2;MLEAF=0.667;MQ=52.20;MQRankSum=-4.881;QD=20.03;ReadPosRankSum=0.009;SOR=1.162	GT:AD:DP:GQ:PL	0/1/1:26,30:56:12:1132,12,0,986
+20	10088799	.	G	A	1037	.	AC=2;AF=0.667;AN=3;BaseQRankSum=5.503;DP=54;FS=10.098;MLEAC=2;MLEAF=0.667;MQ=53.34;MQRankSum=-2.498;QD=19.57;ReadPosRankSum=1.075;SOR=1.003	GT:AD:DP:GQ:PL	0/1/1:22,31:53:27:1047,27,0,617
+20	10088895	.	C	T	554.06	.	AC=1;AF=0.333;AN=3;BaseQRankSum=2.330;DP=43;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=57.80;MQRankSum=0.260;QD=13.85;ReadPosRankSum=1.238;SOR=0.727	GT:AD:DP:GQ:PL	0/0/1:22,18:40:13:560,0,13,647
+20	10088968	.	C	CAAA	1191.75	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.552;DP=77;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=52.81;MQRankSum=-5.145;QD=18.62;ReadPosRankSum=0.629;SOR=0.693	GT:AD:DP:GQ:PL	0/0/1:32,32:64:0:1197,0,0,1220
+20	10088980	.	T	C	1259.05	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.585;DP=74;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=51.42;MQRankSum=-5.018;QD=17.25;ReadPosRankSum=1.577;SOR=0.758	GT:AD:DP:GQ:PL	0/0/1:39,34:73:15:1265,0,15,1486
+20	10088985	.	T	C	1197.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.192;DP=77;FS=0.890;MLEAC=1;MLEAF=0.333;MQ=51.29;MQRankSum=-5.248;QD=16.18;ReadPosRankSum=1.452;SOR=0.742	GT:AD:DP:GQ:PL	0/0/1:42,32:74:30:1203,0,30,1595
+20	10089441	.	A	G	1182.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-4.885;DP=79;FS=6.071;MLEAC=1;MLEAF=0.333;MQ=59.71;MQRankSum=-0.948;QD=15.57;ReadPosRankSum=-0.156;SOR=1.363	GT:AD:DP:GQ:PL	0/1/1:37,39:76:6:1192,6,0,1297
+20	10089525	.	C	T	1554.96	.	AC=2;AF=0.667;AN=3;BaseQRankSum=5.859;DP=83;FS=4.260;MLEAC=2;MLEAF=0.667;MQ=59.50;MQRankSum=1.531;QD=19.20;ReadPosRankSum=0.862;SOR=0.617	GT:AD:DP:GQ:PL	0/1/1:38,43:81:16:1565,16,0,1075
+20	10090289	.	CA	C	429.02	.	AC=2;AF=0.667;AN=3;BaseQRankSum=0.296;DP=88;FS=1.377;MLEAC=1;MLEAF=0.333;MQ=59.97;MQRankSum=1.531;QD=11.29;ReadPosRankSum=0.535;SOR=1.127	GT:AD:DP:GQ:PL	0/1/1:14,24:38:28:426,28,0,235
+20	10090764	.	A	G	855.04	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-2.659;DP=67;FS=4.975;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=13.57;ReadPosRankSum=1.207;SOR=0.310	GT:AD:DP:GQ:PL	0/0/1:34,29:63:16:861,0,16,1199
+20	10090970	.	T	C	1263.05	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-0.484;DP=70;FS=0.927;MLEAC=2;MLEAF=0.667;MQ=59.47;MQRankSum=1.509;QD=18.31;ReadPosRankSum=-0.072;SOR=0.518	GT:AD:DP:GQ:PL	0/1/1:33,36:69:10:1273,10,0,1080
+20	10091214	.	C	T	1255.94	.	AC=2;AF=0.667;AN=3;BaseQRankSum=0.361;DP=73;FS=0.000;MLEAC=2;MLEAF=0.667;MQ=59.74;MQRankSum=-0.916;QD=17.94;ReadPosRankSum=-0.035;SOR=0.625	GT:AD:DP:GQ:PL	0/1/1:33,37:70:12:1266,12,0,1098
+20	10092415	.	A	G	1637.14	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-6.731;DP=103;FS=0.741;MLEAC=1;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=16.21;ReadPosRankSum=0.082;SOR=0.665	GT:AD:DP:GQ:PL	0/0/1:52,49:101:8:1643,0,8,1880
+20	10092927	.	G	T	180.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-2.507;DP=83;FS=60.191;MLEAC=1;MLEAF=0.333;MQ=59.16;MQRankSum=-3.009;QD=2.50;ReadPosRankSum=-0.220;SOR=5.279	GT:AD:DP:GQ:PL	0/0/1:59,13:72:99:186,0,136,1914
+20	10093568	.	GT	G,GTT	381.96	.	AC=1,1;AF=0.333,0.333;AN=3;BaseQRankSum=1.038;DP=62;FS=0.000;MLEAC=1,1;MLEAF=0.333,0.333;MQ=58.80;MQRankSum=0.965;QD=9.09;ReadPosRankSum=0.911;SOR=0.824	GT:AD:DP:GQ:PL	0/1/2:17,21,4:42:39:395,39,42,417,371,0,306,460,353,938
+20	10093923	.	T	A	1086.12	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.667;DP=73;FS=0.924;MLEAC=1;MLEAF=0.333;MQ=59.25;MQRankSum=0.358;QD=16.21;ReadPosRankSum=-1.583;SOR=0.772	GT:AD:DP:GQ:PL	0/0/1:35,32:67:9:1092,0,9,1244
+20	10094251	.	T	A	1290	.	AC=2;AF=0.667;AN=3;BaseQRankSum=0.251;DP=67;FS=11.483;MLEAC=2;MLEAF=0.667;MQ=60.00;MQRankSum=0.000;QD=20.81;ReadPosRankSum=1.806;SOR=1.211	GT:AD:DP:GQ:PL	0/1/1:26,36:62:32:1300,32,0,781
+20	10094582	.	A	G	942.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.388;DP=73;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=59.43;MQRankSum=1.270;QD=13.65;ReadPosRankSum=-0.018;SOR=0.772	GT:AD:DP:GQ:PL	0/0/1:39,30:69:27:948,0,27,1346
+20	10094774	.	C	T	1048.04	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.784;DP=81;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=59.43;MQRankSum=0.962;QD=13.97;ReadPosRankSum=0.197;SOR=0.690	GT:AD:DP:GQ:PL	0/0/1:40,35:75:16:1054,0,16,1271
+20	10095432	.	GTGATGATGA	G	862.06	.	AC=1;AF=0.333;AN=3;BaseQRankSum=1.063;DP=79;FS=1.102;MLEAC=1;MLEAF=0.333;MQ=54.53;MQRankSum=-4.431;QD=17.24;ReadPosRankSum=0.396;SOR=0.460	GT:AD:DP:GQ:PL	0/0/1:27,23:50:10:868,0,10,993
+20	10095741	.	A	G	1084.17	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.534;DP=72;FS=4.721;MLEAC=1;MLEAF=0.333;MQ=57.39;MQRankSum=-2.313;QD=15.49;ReadPosRankSum=-0.500;SOR=0.515	GT:AD:DP:GQ:PL	0/0/1:36,34:70:7:1090,0,7,1218
+20	10096293	.	C	T	1358.56	.	AC=2;AF=0.667;AN=3;BaseQRankSum=4.664;DP=79;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=58.64;MQRankSum=1.397;QD=18.11;ReadPosRankSum=-1.135;SOR=0.638	GT:AD:DP:GQ:PL	0/1/1:37,38:75:3:1366,3,0,1240
+20	10096596	.	C	T	1568.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=2.728;DP=91;FS=0.000;MLEAC=2;MLEAF=0.667;MQ=58.82;MQRankSum=0.612;QD=18.03;ReadPosRankSum=-0.170;SOR=0.640	GT:AD:DP:GQ:PL	0/1/1:40,47:87:20:1579,20,0,1261
+20	10096768	.	A	C	1687.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-2.764;DP=96;FS=3.983;MLEAC=2;MLEAF=0.667;MQ=59.28;MQRankSum=-1.609;QD=18.55;ReadPosRankSum=0.613;SOR=0.445	GT:AD:DP:GQ:PL	0/1/1:42,49:91:21:1698,21,0,1440
+20	10096899	.	G	T	1617.18	.	AC=2;AF=0.667;AN=3;BaseQRankSum=2.755;DP=84;FS=13.441;MLEAC=2;MLEAF=0.667;MQ=59.28;MQRankSum=-1.677;QD=19.48;ReadPosRankSum=0.422;SOR=1.954	GT:AD:DP:GQ:PL	0/1/1:40,43:83:9:1627,9,0,1503
+20	10096905	.	TA	T	1610.75	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.755;DP=86;FS=11.056;MLEAC=1;MLEAF=0.333;MQ=59.30;MQRankSum=-1.739;QD=18.73;ReadPosRankSum=0.461;SOR=1.761	GT:AD:DP:GQ:PL	0/0/1:43,43:86:0:1616,0,0,1601
+20	10096933	.	G	C	1521.04	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.914;DP=89;FS=19.713;MLEAC=1;MLEAF=0.333;MQ=59.32;MQRankSum=-1.840;QD=17.09;ReadPosRankSum=0.383;SOR=1.420	GT:AD:DP:GQ:PL	0/0/1:47,42:89:16:1527,0,16,1749
+20	10096958	.	G	A	1769.94	.	AC=2;AF=0.667;AN=3;BaseQRankSum=2.697;DP=93;FS=19.322;MLEAC=2;MLEAF=0.667;MQ=59.35;MQRankSum=-1.664;QD=19.24;ReadPosRankSum=-1.593;SOR=1.431	GT:AD:DP:GQ:PL	0/1/1:44,48:92:12:1780,12,0,1604
+20	10097075	.	T	G	1445.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-2.533;DP=96;FS=6.613;MLEAC=2;MLEAF=0.667;MQ=58.14;MQRankSum=-1.389;QD=15.72;ReadPosRankSum=0.235;SOR=0.628	GT:AD:DP:GQ:PL	0/1/1:44,48:92:11:1456,11,0,1464
+20	10097101	.	C	CTTT	1116.97	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-0.954;DP=81;FS=7.014;MLEAC=1;MLEAF=0.333;MQ=58.04;MQRankSum=-1.720;QD=16.67;ReadPosRankSum=3.010;SOR=0.519	GT:AD:DP:GQ:PL	0/1/1:33,34:67:2:1117,2,0,1201
+20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C	1097.98	.	AC=1;AF=0.333;AN=3;BaseQRankSum=1.650;DP=90;FS=1.851;MLEAC=1;MLEAF=0.333;MQ=54.34;MQRankSum=-6.464;QD=12.34;ReadPosRankSum=-3.097;SOR=0.948	GT:AD:DP:GQ:PL	0/0/1:57,32:89:75:1104,0,75,2258
+20	10097437	.	TTTTC	*,T	940.61	.	AC=1,2;AF=0.333,0.667;AN=3;DP=78;FS=0.000;MLEAC=1,2;MLEAF=0.333,0.667;MQ=53.68;QD=17.10;SOR=1.877	GT:AD:DP:GQ:PL	1/2/2:0,32,23:55:42:2124,965,945,1801,1234,70,42,1164,0,1123
+20	10097626	.	C	A	649.03	.	AC=1;AF=0.333;AN=3;BaseQRankSum=1.085;DP=54;FS=2.701;MLEAC=1;MLEAF=0.333;MQ=58.00;MQRankSum=-1.331;QD=13.52;ReadPosRankSum=1.015;SOR=0.324	GT:AD:DP:GQ:PL	0/0/1:28,20:48:23:655,0,23,957
+20	10097789	.	T	C	713.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.157;DP=60;FS=5.374;MLEAC=1;MLEAF=0.333;MQ=58.05;MQRankSum=-2.805;QD=12.51;ReadPosRankSum=0.220;SOR=0.756	GT:AD:DP:GQ:PL	0/0/1:34,23:57:33:719,0,33,1192
+20	10097928	.	G	A	583.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-1.203;DP=37;FS=1.315;MLEAC=1;MLEAF=0.333;MQ=58.11;MQRankSum=-1.654;QD=16.22;ReadPosRankSum=-0.079;SOR=0.951	GT:AD:DP:GQ:PL	0/1/1:17,19:36:6:593,6,0,580
+20	10098110	.	G	C	603.21	.	AC=1;AF=0.333;AN=3;BaseQRankSum=2.510;DP=36;FS=6.658;MLEAC=1;MLEAF=0.333;MQ=58.71;MQRankSum=-1.477;QD=16.76;ReadPosRankSum=-0.730;SOR=0.069	GT:AD:DP:GQ:PL	0/0/1:19,17:36:6:609,0,6,721
+20	10098135	.	C	A	500.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.155;DP=39;FS=4.449;MLEAC=1;MLEAF=0.333;MQ=59.65;MQRankSum=1.563;QD=12.82;ReadPosRankSum=-0.591;SOR=0.070	GT:AD:DP:GQ:PL	0/0/1:25,14:39:33:506,0,33,971
+20	10098219	.	TATATATA	T	327.08	.	AC=1;AF=0.333;AN=3;BaseQRankSum=3.147;DP=21;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=55.94;MQRankSum=-0.205;QD=15.58;ReadPosRankSum=0.427;SOR=0.465	GT:AD:DP:GQ:PL	0/0/1:12,9:21:9:333,0,9,460
+20	10098237	.	A	T	263.79	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.006;DP=14;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=53.89;MQRankSum=-1.885;QD=18.84;ReadPosRankSum=1.118;SOR=0.693	GT:AD:DP:GQ:PL	0/0/1:7,7:14:0:269,0,0,269
+20	10098265	.	T	C	153.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=1.834;DP=6;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=41.96;MQRankSum=-1.834;QD=25.66;ReadPosRankSum=0.842;SOR=1.329	GT:AD:DP:GQ:PL	0/1/1:2,4:6:6:163,6,0,60
+20	10098885	.	C	CA	462.08	.	AC=1;AF=0.333;AN=3;BaseQRankSum=0.165;DP=33;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=49.73;MQRankSum=-4.449;QD=14.91;ReadPosRankSum=-0.954;SOR=0.518	GT:AD:DP:GQ:PL	0/0/1:17,14:31:9:468,0,9,569
+20	10098945	.	T	C	426.92	.	AC=2;AF=0.667;AN=3;BaseQRankSum=1.475;DP=22;FS=3.882;MLEAC=2;MLEAF=0.667;MQ=51.15;MQRankSum=-2.504;QD=19.41;ReadPosRankSum=1.038;SOR=2.368	GT:AD:DP:GQ:PL	0/1/1:9,13:22:13:437,13,0,249
+20	10098987	.	C	T	394.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=3.127;DP=25;FS=7.005;MLEAC=1;MLEAF=0.333;MQ=51.36;MQRankSum=-2.734;QD=16.46;ReadPosRankSum=0.436;SOR=2.925	GT:AD:DP:GQ:PL	0/1/1:11,13:24:6:404,6,0,347
+20	10099029	.	T	C	363.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.809;DP=30;FS=1.987;MLEAC=1;MLEAF=0.333;MQ=52.93;MQRankSum=-3.731;QD=12.52;ReadPosRankSum=-1.224;SOR=1.609	GT:AD:DP:GQ:PL	0/0/1:19,10:29:27:369,0,27,774
+20	10099034	.	C	A	363.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=2.757;DP=29;FS=1.987;MLEAC=1;MLEAF=0.333;MQ=53.57;MQRankSum=-3.731;QD=12.52;ReadPosRankSum=-1.850;SOR=1.609	GT:AD:DP:GQ:PL	0/0/1:19,10:29:27:369,0,27,774
+20	10099044	.	A	C	363.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.148;DP=29;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=51.81;MQRankSum=-4.533;QD=12.52;ReadPosRankSum=-2.207;SOR=0.892	GT:AD:DP:GQ:PL	0/0/1:19,10:29:27:369,0,27,774
+20	10099046	.	T	C	330.03	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-2.165;DP=24;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=49.94;MQRankSum=-4.418;QD=13.75;ReadPosRankSum=-2.297;SOR=0.515	GT:AD:DP:GQ:PL	0/0/1:15,9:24:18:336,0,18,606
+20	10099055	.	T	C	286.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.554;DP=25;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=50.20;MQRankSum=-4.179;QD=11.44;ReadPosRankSum=-1.970;SOR=0.770	GT:AD:DP:GQ:PL	0/0/1:17,8:25:27:292,0,27,680
+20	10099079	.	C	T	159.02	.	AC=1;AF=0.333;AN=3;BaseQRankSum=1.434;DP=30;FS=1.826;MLEAC=1;MLEAF=0.333;MQ=51.49;MQRankSum=-2.614;QD=5.30;ReadPosRankSum=0.969;SOR=1.329	GT:AD:DP:GQ:PL	0/0/1:24,6:30:54:165,0,54,906
+20	10099111	.	T	TTTTGTTTG	683.03	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.207;DP=52;FS=1.206;MLEAC=1;MLEAF=0.333;MQ=53.85;MQRankSum=-0.973;QD=16.26;ReadPosRankSum=-1.860;SOR=0.967	GT:AD:DP:GQ:PL	0/0/1:23,19:42:12:689,0,12,798
+20	10099140	.	G	T	1012.36	.	AC=2;AF=0.667;AN=3;BaseQRankSum=-0.114;DP=64;FS=2.241;MLEAC=1;MLEAF=0.333;MQ=55.86;MQRankSum=-2.469;QD=16.33;ReadPosRankSum=0.846;SOR=1.114	GT:AD:DP:GQ:PL	0/1/1:30,32:62:8:1022,8,0,920
+20	10099190	.	G	T	1042.41	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-0.034;DP=65;FS=0.000;MLEAC=1;MLEAF=0.333;MQ=57.56;MQRankSum=-1.711;QD=16.04;ReadPosRankSum=-1.260;SOR=0.776	GT:AD:DP:GQ:PL	0/0/1:33,32:65:3:1048,0,3,1139
+20	10099220	.	A	G	596.04	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-1.664;DP=47;FS=1.137;MLEAC=1;MLEAF=0.333;MQ=57.74;MQRankSum=-2.596;QD=13.25;ReadPosRankSum=0.629;SOR=0.519	GT:AD:DP:GQ:PL	0/0/1:25,20:45:16:602,0,16,870
+20	10099250	.	G	A	716.96	.	AC=2;AF=0.667;AN=3;BaseQRankSum=3.170;DP=39;FS=7.195;MLEAC=2;MLEAF=0.667;MQ=56.89;MQRankSum=-2.272;QD=19.38;ReadPosRankSum=0.583;SOR=0.162	GT:AD:DP:GQ:PL	0/1/1:16,21:37:16:727,16,0,422
+20	10099535	.	G	A	1357.01	.	AC=2;AF=0.667;AN=3;BaseQRankSum=5.034;DP=68;FS=2.172;MLEAC=2;MLEAF=0.667;MQ=59.04;MQRankSum=-1.418;QD=20.88;ReadPosRankSum=-0.777;SOR=0.408	GT:AD:DP:GQ:PL	0/1/1:26,39:65:39:1367,39,0,689
+20	10099565	.	C	T	1356.98	.	AC=2;AF=0.667;AN=3;BaseQRankSum=4.595;DP=70;FS=8.736;MLEAC=2;MLEAF=0.667;MQ=59.40;MQRankSum=-1.266;QD=19.67;ReadPosRankSum=1.225;SOR=0.191	GT:AD:DP:GQ:PL	0/1/1:31,38:69:21:1367,21,0,986
+20	10099755	.	C	T	1105.41	.	AC=1;AF=0.333;AN=3;BaseQRankSum=1.550;DP=66;FS=2.074;MLEAC=1;MLEAF=0.333;MQ=59.37;MQRankSum=-0.022;QD=17.01;ReadPosRankSum=-0.230;SOR=0.446	GT:AD:DP:GQ:PL	0/0/1:33,32:65:3:1111,0,3,1133
+20	10099832	.	A	G	1087.03	.	AC=1;AF=0.333;AN=3;BaseQRankSum=-4.563;DP=75;FS=4.632;MLEAC=1;MLEAF=0.333;MQ=59.00;MQRankSum=0.869;QD=15.10;ReadPosRankSum=-1.023;SOR=0.871	GT:AD:DP:GQ:PL	0/0/1:39,33:72:18:1093,0,18,1421
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testMismatchPloidyRegions.bed b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testMismatchPloidyRegions.bed
new file mode 100644
index 00000000000..9cec9490ffe
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testMismatchPloidyRegions.bed
@@ -0,0 +1,3 @@
+chr20	10000000	10010000	2
+20	10020000	10030000	4
+20	10060000	10080000	1
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNegativePloidyRegions.bed b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNegativePloidyRegions.bed
new file mode 100644
index 00000000000..0020760881a
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNegativePloidyRegions.bed
@@ -0,0 +1,3 @@
+20	10000000	10010000	-2
+20	10020000	10030000	4
+20	10060000	10080000	1
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNonIntegerPloidyRegions.bed b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNonIntegerPloidyRegions.bed
new file mode 100644
index 00000000000..c294c72b668
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testNonIntegerPloidyRegions.bed
@@ -0,0 +1,3 @@
+20	10000000	10010000	hi
+20	10020000	10030000	.
+20	10060000	10080000	1
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testPloidyRegions.bed b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testPloidyRegions.bed
new file mode 100644
index 00000000000..2e652e2566b
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testPloidyRegions.bed
@@ -0,0 +1,4 @@
+20	10000000	10010000	2
+20	10020000	10030000	4
+20  10022000    10026000    2
+20	10060000	10080000	1

From a40ba3e7f9bcbdbc6dbf932cb15bd42236b73d65 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Thu, 7 Dec 2023 11:38:09 -0500
Subject: [PATCH 2/5] Extracted a cache of Genotypers indexed by ploidy (#8598)

* Introduced a new class MulitPloidyGenotyperCache which keeps track of multiple GenotypingEngines that have different ploidy values.
* minor refactoring in related classes
* removed an unused type parameter from GenotypingEngine
---
 .../tools/walkers/GenotypeGVCFsEngine.java    |   4 +-
 ...GenotypeCalculationArgumentCollection.java |   2 +-
 .../walkers/genotyper/GenotypingEngine.java   |  65 +++++-----
 .../genotyper/MinimalGenotypingEngine.java    |  10 +-
 .../StandardCallerArgumentCollection.java     |   5 +-
 .../haplotypecaller/AlleleFilteringHC.java    |   2 +-
 .../HaplotypeCallerEngine.java                | 121 ++++++------------
 .../HaplotypeCallerGenotypingEngine.java      |  10 +-
 .../MultiPloidyGenotyperCache.java            |  73 +++++++++++
 .../ReducibleAnnotationBaseTest.java          |   2 +-
 .../genotyper/GenotypingEngineUnitTest.java   |   4 +-
 .../HaplotypeCallerIntegrationTest.java       |  19 +--
 .../MultiPloidyGenotyperCacheUnitTest.java    |  82 ++++++++++++
 13 files changed, 253 insertions(+), 146 deletions(-)
 create mode 100644 src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java
 create mode 100644 src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
index 312a90872e7..f7f5f0ba9ef 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
@@ -45,7 +45,7 @@ public class GenotypeGVCFsEngine
     private VariantAnnotatorEngine annotationEngine = null;
 
     //the genotyping engine
-    private GenotypingEngine<?> forceOutputGenotypingEngine = null;
+    private GenotypingEngine forceOutputGenotypingEngine = null;
     private MinimalGenotypingEngine genotypingEngine = null;
 
     // the INFO field annotation key names to remove
@@ -303,7 +303,7 @@ private VariantContext callSomaticGenotypes(final VariantContext vc, double tlod
         final VariantContextBuilder builder = new VariantContextBuilder(vc);
         final VariantContext regenotypedVC = builder.genotypes(newGenotypes).make();
 
-        final int maxAltAlleles = genotypingEngine.getConfiguration().genotypeArgs.maxAlternateAlleles;
+        final int maxAltAlleles = genotypingEngine.getGenotypeArgs().maxAlternateAlleles;
         List<Allele> allelesToKeep;
 
         //we need to make sure all alleles pass the tlodThreshold
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
index 5090a87c484..75ba3d7784f 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
@@ -71,7 +71,7 @@ public GenotypeCalculationArgumentCollection clone() {
      * Using this argument instructs the genotyper to annotate (in the INFO field) the number of alternate alleles that were originally discovered at the site.
      */
     @Argument(fullName = "annotate-with-num-discovered-alleles", doc = "If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site", optional = true)
-    public boolean ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = false;
+    public boolean annotateNumberOfAllelesDiscovered = false;
 
     /**
      * The expected heterozygosity value used to compute prior probability that a locus is non-reference.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
index 1846fbe806d..3121b71e873 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
@@ -28,13 +28,13 @@
 /**
  * Base class for genotyper engines.
  */
-public abstract class GenotypingEngine<Config extends StandardCallerArgumentCollection> {
+public abstract class GenotypingEngine {
 
     private final static int TOO_LONG_PL = 100000;
 
     protected final AlleleFrequencyCalculator alleleFrequencyCalculator;
 
-    protected final Config configuration;
+    private final StandardCallerArgumentCollection configuration;
 
     protected VariantAnnotatorEngine annotationEngine;
 
@@ -63,7 +63,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
      *
      * @throws IllegalArgumentException if any of {@code samples}, {@code configuration} is {@code null} or if {@code samples} is empty.
      */
-    protected GenotypingEngine(final Config configuration,
+    protected GenotypingEngine(final StandardCallerArgumentCollection configuration,
                                final SampleList samples,
                                final boolean doAlleleSpecificCalcs) {
         this.configuration = Utils.nonNull(configuration, "the configuration cannot be null");
@@ -89,12 +89,16 @@ public void setLogger(final Logger logger) {
 
     public Set<VCFInfoHeaderLine> getAppropriateVCFInfoHeaders() {
         final Set<VCFInfoHeaderLine> headerInfo = new LinkedHashSet<>();
-        if ( configuration.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) {
+        if ( getGenotypeArgs().annotateNumberOfAllelesDiscovered) {
             headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NUMBER_OF_DISCOVERED_ALLELES_KEY));
         }
         return headerInfo;
     }
 
+    public GenotypeCalculationArgumentCollection getGenotypeArgs() {
+        return getConfiguration().genotypeArgs;
+    }
+
     /**
      * Changes the annotation engine for this genotyping-engine.
      *
@@ -109,7 +113,7 @@ public void setAnnotationEngine(final VariantAnnotatorEngine annotationEngine) {
      *
      * @return never {@code null}.
      */
-    public Config getConfiguration() {
+    protected StandardCallerArgumentCollection getConfiguration() {
         return configuration;
     }
 
@@ -131,8 +135,8 @@ public VariantContext calculateGenotypes(final VariantContext vc, final Genotype
             return null;
         }
 
-        final int defaultPloidy = configuration.genotypeArgs.samplePloidy;
-        final int maxAltAlleles = configuration.genotypeArgs.maxAlternateAlleles;
+        final int defaultPloidy = getGenotypeArgs().samplePloidy;
+        final int maxAltAlleles = getGenotypeArgs().maxAlternateAlleles;
 
         VariantContext reducedVC = vc;
         if (maxAltAlleles < vc.getAlternateAlleles().size()) {
@@ -156,7 +160,7 @@ public VariantContext calculateGenotypes(final VariantContext vc, final Genotype
 
         // note the math.abs is necessary because -10 * 0.0 => -0.0 which isn't nice
         final double log10Confidence =
-                    !outputAlternativeAlleles.siteIsMonomorphic || configuration.annotateAllSitesWithPLs
+                    !outputAlternativeAlleles.siteIsMonomorphic || getConfiguration().annotateAllSitesWithPLs
                             ? AFresult.log10ProbOnlyRefAlleleExists() + 0.0 : AFresult.log10ProbVariantPresent() + 0.0;
 
         // Add 0.0 removes -0.0 occurrences.
@@ -188,11 +192,11 @@ && noAllelesOrFirstAlleleIsNotNonRef(outputAlternativeAlleles.alleles) && forced
         // create the genotypes
         //TODO: omit subsetting if output alleles is not a proper subset of vc.getAlleles
         final GenotypesContext genotypes = outputAlleles.size() == 1 ? GATKVariantContextUtils.subsetToRefOnly(vc, defaultPloidy) :
-                AlleleSubsettingUtils.subsetAlleles(vc.getGenotypes(), defaultPloidy, vc.getAlleles(), outputAlleles, gpc, configuration.genotypeArgs.genotypeAssignmentMethod);
+                AlleleSubsettingUtils.subsetAlleles(vc.getGenotypes(), defaultPloidy, vc.getAlleles(), outputAlleles, gpc, getGenotypeArgs().genotypeAssignmentMethod);
 
-        if (configuration.genotypeArgs.usePosteriorProbabilitiesToCalculateQual && hasPosteriors(genotypes)) {
+        if (getGenotypeArgs().usePosteriorProbabilitiesToCalculateQual && hasPosteriors(genotypes)) {
             final double log10NoVariantPosterior = phredNoVariantPosteriorProbability(outputAlleles, genotypes) * -.1;
-            final double qualUpdate = !outputAlternativeAlleles.siteIsMonomorphic || configuration.annotateAllSitesWithPLs
+            final double qualUpdate = !outputAlternativeAlleles.siteIsMonomorphic || getConfiguration().annotateAllSitesWithPLs
                     ? log10NoVariantPosterior + 0.0 : MathUtils.log10OneMinusPow10(log10NoVariantPosterior) + 0.0;
             if (!Double.isNaN(qualUpdate)) {
                 builder.log10PError(qualUpdate);
@@ -260,30 +264,23 @@ static boolean noAllelesOrFirstAlleleIsNotNonRef(List<Allele> altAlleles) {
     protected abstract String callSourceString();
 
     /**
-     * Holds information about the alternative allele subsetting based on supporting evidence, genotyping and
-     * output modes.
-     */
-    private static class OutputAlleleSubset {
-        private  final List<Allele> alleles;
-        private  final boolean siteIsMonomorphic;
-        private  final List<Integer> mleCounts;
-
-        private OutputAlleleSubset(final List<Allele> alleles, final List<Integer> mleCounts, final boolean siteIsMonomorphic) {
+         * Holds information about the alternative allele subsetting based on supporting evidence, genotyping and
+         * output modes.
+         */
+        private record OutputAlleleSubset(List<Allele> alleles, List<Integer> mleCounts, boolean siteIsMonomorphic) {
+        private OutputAlleleSubset {
             Utils.nonNull(alleles, "alleles");
             Utils.nonNull(mleCounts, "mleCounts");
-            this.siteIsMonomorphic = siteIsMonomorphic;
-            this.alleles = alleles;
-            this.mleCounts = mleCounts;
         }
 
-        private List<Allele> outputAlleles(final Allele referenceAllele) {
-            return Stream.concat(Stream.of(referenceAllele), alleles.stream()).collect(Collectors.toList());
-        }
+            private List<Allele> outputAlleles(final Allele referenceAllele) {
+                return Stream.concat(Stream.of(referenceAllele), alleles.stream()).collect(Collectors.toList());
+            }
 
-        public List<Integer> alternativeAlleleMLECounts() {
-            return mleCounts;
+            public List<Integer> alternativeAlleleMLECounts() {
+                return mleCounts;
+            }
         }
-    }
 
 
     /**
@@ -308,7 +305,7 @@ private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalculationResult
                 // we want to keep the NON_REF symbolic allele but only in the absence of a non-symbolic allele, e.g.
                 // if we combined a ref / NON_REF gVCF with a ref / alt gVCF
                 final boolean isNonRefWhichIsLoneAltAllele = alternativeAlleleCount == 1 && allele.equals(Allele.NON_REF_ALLELE);
-                final boolean isPlausible = afCalculationResult.passesThreshold(allele, configuration.genotypeArgs.standardConfidenceForCalling);
+                final boolean isPlausible = afCalculationResult.passesThreshold(allele, getGenotypeArgs().standardConfidenceForCalling);
 
                 //it's possible that the upstream deletion that spanned this site was not emitted, mooting the symbolic spanning deletion allele
                 final boolean isSpuriousSpanningDeletion = GATKVCFConstants.isSpanningDeletion(allele) && !isVcCoveredByDeletion(vc);
@@ -415,16 +412,16 @@ protected final boolean cannotBeGenotyped(final VariantContext vc) {
      * This does not necessarily emit calls for all sites in a region (see {@link OutputMode}).
      */
     protected boolean emitAllActiveSites() {
-        return configuration.outputMode == OutputMode.EMIT_ALL_ACTIVE_SITES;
+        return getConfiguration().outputMode == OutputMode.EMIT_ALL_ACTIVE_SITES;
     }
 
     protected final boolean passesEmitThreshold(final double conf, final boolean bestGuessIsRef) {
-        return (configuration.outputMode == OutputMode.EMIT_ALL_CONFIDENT_SITES || !bestGuessIsRef) &&
+        return (getConfiguration().outputMode == OutputMode.EMIT_ALL_CONFIDENT_SITES || !bestGuessIsRef) &&
                 passesCallThreshold(conf);
     }
 
     protected final boolean passesCallThreshold(final double conf) {
-        return conf >= configuration.genotypeArgs.standardConfidenceForCalling;
+        return conf >= getGenotypeArgs().standardConfidenceForCalling;
     }
 
     protected Map<String,Object> composeCallAttributes(final VariantContext vc, final List<Integer> alleleCountsofMLE,
@@ -457,7 +454,7 @@ protected Map<String,Object> composeCallAttributes(final VariantContext vc, fina
             attributes.put(GATKVCFConstants.AS_QUAL_KEY, perAlleleQuals.stream().mapToInt(q -> Math.round(q)).boxed().collect(Collectors.toList()));
         }
 
-        if ( configuration.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) {
+        if ( getGenotypeArgs().annotateNumberOfAllelesDiscovered) {
             attributes.put(GATKVCFConstants.NUMBER_OF_DISCOVERED_ALLELES_KEY, vc.getAlternateAlleles().size());
         }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java
index 4d5b3986e91..a72442bda9e 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java
@@ -19,7 +19,7 @@
  * used only by the HaplotypeCaller for its isActive() determination. Should not be used for
  * any other purpose!
  */
-public final class MinimalGenotypingEngine extends GenotypingEngine<StandardCallerArgumentCollection> {
+public final class MinimalGenotypingEngine extends GenotypingEngine {
 
     private final DragstrParams dragstrParams;
 
@@ -61,7 +61,7 @@ public MinimalGenotypingEngine(final StandardCallerArgumentCollection configurat
 
     @Override
     protected boolean forceKeepAllele(final Allele allele) {
-        return configuration.annotateAllSitesWithPLs;
+        return getConfiguration().annotateAllSitesWithPLs;
     }
 
     @Override
@@ -71,8 +71,8 @@ protected String callSourceString() {
 
     @Override
     public VariantContext calculateGenotypes(final VariantContext vc) {
-        if (dragstrParams == null || getConfiguration().genotypeArgs.dontUseDragstrPriors || !GATKVariantContextUtils.containsInlineIndel(vc) || referenceContext == null) {
-            final GenotypePriorCalculator gpc = GenotypePriorCalculator.assumingHW(configuration.genotypeArgs);
+        if (dragstrParams == null || getGenotypeArgs().dontUseDragstrPriors || !GATKVariantContextUtils.containsInlineIndel(vc) || referenceContext == null) {
+            final GenotypePriorCalculator gpc = GenotypePriorCalculator.assumingHW(getGenotypeArgs());
             return calculateGenotypes(vc, gpc, Collections.emptyList());
         } else {
 
@@ -90,7 +90,7 @@ public VariantContext calculateGenotypes(final VariantContext vc) {
             final int period = analyzer.period(startOffset);
             final int repeats = analyzer.repeatLength(startOffset);
 
-            final GenotypePriorCalculator gpc = GenotypePriorCalculator.givenDragstrParams(dragstrParams, period, repeats, Math.log10(getConfiguration().genotypeArgs.snpHeterozygosity), 2.0);
+            final GenotypePriorCalculator gpc = GenotypePriorCalculator.givenDragstrParams(dragstrParams, period, repeats, Math.log10(getGenotypeArgs().snpHeterozygosity), 2.0);
             return  calculateGenotypes(vc, gpc, Collections.emptyList());
         }
     }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java
index a6b25ed7c53..0ca6a19975e 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java
@@ -2,6 +2,7 @@
 
 import htsjdk.variant.variantcontext.VariantContext;
 import org.apache.commons.collections4.map.DefaultedMap;
+import org.apache.commons.lang3.SerializationUtils;
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
@@ -17,7 +18,7 @@
 /**
  * This is pulled out so that every caller isn't exposed to the arguments from every other caller.
  */
-public class StandardCallerArgumentCollection implements Serializable {
+public final class StandardCallerArgumentCollection implements Serializable {
     private static final long serialVersionUID = 1L;
 
     /**
@@ -28,7 +29,7 @@ public class StandardCallerArgumentCollection implements Serializable {
     public void copyStandardCallerArgsFrom( final StandardCallerArgumentCollection other ) {
         Utils.nonNull(other);
 
-        this.genotypeArgs = other.genotypeArgs.clone();
+        this.genotypeArgs = SerializationUtils.clone(other.genotypeArgs);
         this.CONTAMINATION_FRACTION = other.CONTAMINATION_FRACTION;
         this.CONTAMINATION_FRACTION_FILE = other.CONTAMINATION_FRACTION_FILE != null ? new File(other.CONTAMINATION_FRACTION_FILE.getAbsolutePath()) : null;
         if ( other.sampleContamination != null ) {
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
index 2788cc21575..66b76159ae9 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
@@ -29,7 +29,7 @@ public class AlleleFilteringHC extends AlleleFiltering {
     public AlleleFilteringHC(HaplotypeCallerArgumentCollection _hcargs, OutputStreamWriter assemblyDebugStream, HaplotypeCallerGenotypingEngine _genotypingEngine){
         super(_hcargs, assemblyDebugStream);
         genotypingEngine = _genotypingEngine;
-        GenotypeCalculationArgumentCollection config = genotypingEngine.getConfiguration().genotypeArgs;
+        GenotypeCalculationArgumentCollection config = genotypingEngine.getGenotypeArgs();
          afCalc = AlleleFrequencyCalculator.makeCalculator(config);
     }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
index 0126a49b802..c2262272aaa 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
@@ -6,7 +6,6 @@
 import htsjdk.samtools.util.Locatable;
 import htsjdk.samtools.util.OverlapDetector;
 import htsjdk.samtools.util.RuntimeIOException;
-import htsjdk.tribble.NamedFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
@@ -26,7 +25,6 @@
 import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
 import org.broadinstitute.hellbender.tools.walkers.annotator.*;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod;
-import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection;
@@ -99,16 +97,6 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
      */
     protected final OverlapDetector<SimpleCount> ploidyRegionsOverlapDetector;
 
-    /**
-     * List of all custom ploidies provided by user
-     */
-    private final LinkedHashSet<Integer> allCustomPloidies;
-
-    /**
-     * The default genotyping engine for the isActive() determination
-     */
-    private MinimalGenotypingEngine defaultActiveRegionEvaluationGenotyperEngine = null;
-
     /**
      * Map of user-provided ploidy values to corresponding active region genotyper. Values are checked as valid Integers during
      * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
@@ -122,11 +110,6 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
     // If we are in PDHMM mode we need to hold onto two likelihoods engines for the fallback
     private ReadLikelihoodCalculationEngine pdhmmLikelihoodCalculationEngine = null;
 
-    /**
-     * The default genotyping engine to use for actual variant calling and genotyping in an active region.
-     */
-    protected HaplotypeCallerGenotypingEngine defaultGenotypingEngine = null;
-
     /**
      * Map of user-provided ploidy values to corresponding genotyper. Values are checked as valid Integers during
      * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
@@ -197,6 +180,8 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
 
     private static final Allele FAKE_REF_ALLELE = Allele.create("N", true); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file
     private static final Allele FAKE_ALT_ALLELE = Allele.create("<FAKE_ALT>", false); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file
+    private MultiPloidyGenotyperCache<HaplotypeCallerGenotypingEngine> genotypingEngines;
+    private MultiPloidyGenotyperCache<MinimalGenotypingEngine> activeRegionGenotypingEngines;
 
     /**
      * Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header,
@@ -241,12 +226,11 @@ public HaplotypeCallerEngine(final HaplotypeCallerArgumentCollection hcArgs, Ass
 
         for (SimpleCount region : this.ploidyRegions) {
             if (!IntervalUtils.intervalIsOnDictionaryContig(region.getInterval(), readsHeader.getSequenceDictionary())) {
-                throw new UserException("Invalid region provided for --ploidy-regions at " + region.getContig() + ":" + region.getStart() + "-" + region.getEnd() + ". Contig name or endpoint doesn't match read sequence dictionary.");
+                throw new UserException("Invalid region provided for --" + HaplotypeCallerArgumentCollection.PLOIDY_REGIONS_NAME + " at " + region.getContig() + ":" + region.getStart() + "-" + region.getEnd() + ". Contig name or endpoint doesn't match read sequence dictionary.");
             }
         }
 
         this.ploidyRegionsOverlapDetector = OverlapDetector.create(this.ploidyRegions);
-        this.allCustomPloidies = this.ploidyRegions.stream().map(SimpleCount::getCount).collect(Collectors.toCollection(LinkedHashSet::new));
 
         trimmer = new AssemblyRegionTrimmer(assemblyRegionArgs, readsHeader.getSequenceDictionary());
         initialize(createBamOutIndex, createBamOutMD5);
@@ -294,16 +278,10 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5
 
         initializeActiveRegionEvaluationGenotyperEngine();
 
-        defaultGenotypingEngine = new HaplotypeCallerGenotypingEngine(hcArgs, samplesList, ! hcArgs.doNotRunPhysicalPhasing, hcArgs.applyBQD);
-        defaultGenotypingEngine.setAnnotationEngine(annotationEngine);
-
-        // Create other custom genotyping engines if user provided ploidyRegions
-        for (final int ploidy : this.allCustomPloidies) {
-            HaplotypeCallerArgumentCollection newPloidyHcArgs = hcArgs.copyWithNewPloidy(ploidy);
-            HaplotypeCallerGenotypingEngine newGenotypingEngine = new HaplotypeCallerGenotypingEngine(newPloidyHcArgs, samplesList, ! hcArgs.doNotRunPhysicalPhasing, hcArgs.applyBQD);
-            newGenotypingEngine.setAnnotationEngine(annotationEngine);
-            this.ploidyToGenotyperMap.put(ploidy, newGenotypingEngine);
-        }
+        final int defaultPloidy = hcArgs.standardArgs.genotypeArgs.samplePloidy;
+        genotypingEngines = new MultiPloidyGenotyperCache<>(this::makeGenotypingEngine,
+                defaultPloidy,
+                ploidyRegionsOverlapDetector);
 
         boolean isFlowBased = (hcArgs.likelihoodArgs.likelihoodEngineImplementation == ReadLikelihoodCalculationEngine.Implementation.FlowBased)
                 || (hcArgs.likelihoodArgs.likelihoodEngineImplementation == ReadLikelihoodCalculationEngine.Implementation.FlowBasedHMM);
@@ -357,6 +335,13 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5
                 : null);
     }
 
+    private HaplotypeCallerGenotypingEngine makeGenotypingEngine(int ploidy) {
+        final HaplotypeCallerArgumentCollection newPloidyHcArgs = hcArgs.copyWithNewPloidy(ploidy);
+        final HaplotypeCallerGenotypingEngine newGenotypingEngine = new HaplotypeCallerGenotypingEngine(newPloidyHcArgs, samplesList, !newPloidyHcArgs.doNotRunPhysicalPhasing, newPloidyHcArgs.applyBQD);
+        newGenotypingEngine.setAnnotationEngine(annotationEngine);
+        return newGenotypingEngine;
+    }
+
     private boolean isVCFMode() {
         return hcArgs.emitReferenceConfidence == ReferenceConfidenceMode.NONE;
     }
@@ -432,27 +417,28 @@ private void initializeSamples() {
 
     private void initializeActiveRegionEvaluationGenotyperEngine() {
         final StandardCallerArgumentCollection activeRegionArgs = new StandardCallerArgumentCollection();
+
         activeRegionArgs.copyStandardCallerArgsFrom(hcArgs.standardArgs);
 
         activeRegionArgs.outputMode = OutputMode.EMIT_VARIANTS_ONLY;
         activeRegionArgs.genotypeArgs.standardConfidenceForCalling = Math.min(MAXMIN_CONFIDENCE_FOR_CONSIDERING_A_SITE_AS_POSSIBLE_VARIANT_IN_ACTIVE_REGION_DISCOVERY, hcArgs.standardArgs.genotypeArgs.standardConfidenceForCalling); // low values used for isActive determination only, default/user-specified values used for actual calling
         activeRegionArgs.CONTAMINATION_FRACTION = 0.0;
         activeRegionArgs.CONTAMINATION_FRACTION_FILE = null;
-        // Seems that at least with some test data we can lose genuine haploid variation if we use ploidy == 1
-        activeRegionArgs.genotypeArgs.samplePloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, hcArgs.standardArgs.genotypeArgs.samplePloidy);
-
-        defaultActiveRegionEvaluationGenotyperEngine = new MinimalGenotypingEngine(activeRegionArgs, samplesList);
-        defaultActiveRegionEvaluationGenotyperEngine.setLogger(logger);
-
-        // If custom ploidyRegions provided, create corresponding map for active region determination genotyper
-        for (final int ploidy : this.allCustomPloidies) {
-            StandardCallerArgumentCollection newPloidyActiveArgs = new StandardCallerArgumentCollection();
-            newPloidyActiveArgs.copyStandardCallerArgsFrom(activeRegionArgs);
-            newPloidyActiveArgs.genotypeArgs.samplePloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, ploidy);
-            MinimalGenotypingEngine newActiveGenotypingEngine = new MinimalGenotypingEngine(newPloidyActiveArgs, samplesList);
-            newActiveGenotypingEngine.setLogger(logger);
-            this.ploidyToActiveEvaluationGenotyper.put(ploidy, newActiveGenotypingEngine);
-        }
+
+        final int defaultPloidy = hcArgs.standardArgs.genotypeArgs.samplePloidy;
+        activeRegionGenotypingEngines = new MultiPloidyGenotyperCache<>(ploidy -> {
+                // Seems that at least with some test data we can lose genuine haploid variation if we use ploidy == 1
+                final int adjustedPloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, ploidy);
+                final StandardCallerArgumentCollection newPloidyActiveArgs = new StandardCallerArgumentCollection();
+                newPloidyActiveArgs.copyStandardCallerArgsFrom(activeRegionArgs);
+                newPloidyActiveArgs.genotypeArgs.samplePloidy = adjustedPloidy;
+                final MinimalGenotypingEngine genotyper = new MinimalGenotypingEngine(newPloidyActiveArgs, samplesList);
+                genotyper.setLogger(logger);
+                return genotyper;
+            },
+                defaultPloidy,
+                ploidyRegionsOverlapDetector
+        );
     }
 
     /**
@@ -525,7 +511,7 @@ public VCFHeader makeVCFHeader( final SAMSequenceDictionary sequenceDictionary,
         final Set<VCFHeaderLine> headerInfo = new HashSet<>();
         headerInfo.addAll(defaultToolHeaderLines);
 
-        headerInfo.addAll(defaultGenotypingEngine.getAppropriateVCFInfoHeaders());
+        headerInfo.addAll(genotypingEngines.getDefaultGenotypingEngine().getAppropriateVCFInfoHeaders());
         // all annotation fields from VariantAnnotatorEngine
         headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions(emitReferenceConfidence()));
         // all callers need to add these standard annotation header lines
@@ -593,41 +579,13 @@ public void writeHeader( final VariantContextWriter vcfWriter, final SAMSequence
         vcfWriter.writeHeader(makeVCFHeader(sequenceDictionary, defaultToolHeaderLines));
     }
 
-    /**
-     * Determines the appropriate ploidy to use at given site for different genotyping engines.
-     * @param region Current region of interest
-     * @return Ploidy value to use here given user inputs, or -1 if fall back to default
-     */
-    private int getPloidyToUseAtThisSite(Locatable region) {
-        Set<SimpleCount> overlaps = this.ploidyRegionsOverlapDetector.getOverlaps(region);
-        // Return first engine for interval overlapping this region
-        if (!overlaps.isEmpty()) {
-            Iterator<SimpleCount> intervals = overlaps.iterator();
-            int max = intervals.next().getCount();
-            while (intervals.hasNext()) {
-                int next = intervals.next().getCount();
-                if (next > max) {
-                    max = next;
-                }
-            }
-            return max;
-        } else {
-            return -1; // Sentinel value to fall back to default genotyper
-        }
-    }
-
     /**
      * Selects appropriate active region genotyping engine for given region
      * @param region Current region of interest
      * @return Active genotyping engine with correct ploidy setting for given region
      */
     private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
-        int currentPloidy = getPloidyToUseAtThisSite(region);
-        if (currentPloidy == -1) {
-            return this.defaultActiveRegionEvaluationGenotyperEngine;
-        } else {
-            return this.ploidyToActiveEvaluationGenotyper.get(currentPloidy);
-        }
+        return activeRegionGenotypingEngines.getGenotypingEngine(region);
     }
 
     /**
@@ -636,14 +594,9 @@ private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
      * @return Genotyping engine with correct ploidy setting for given region
      */
     protected HaplotypeCallerGenotypingEngine getLocalGenotypingEngine(Locatable region) {
-        int currentPloidy = getPloidyToUseAtThisSite(region);
-        if (currentPloidy == -1) {
-            return this.defaultGenotypingEngine;
-        } else {
-            return this.ploidyToGenotyperMap.get(currentPloidy);
-        }
+        return genotypingEngines.getGenotypingEngine(region);
     }
-
+    
     /**
      * Given a pileup, returns an ActivityProfileState containing the probability (0.0 to 1.0) that it's an "active" site.
      *
@@ -669,7 +622,7 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
             return new ActivityProfileState(ref.getInterval(), 0.0);
         }
 
-        final int ploidy = localActiveGenotypingEngine.getConfiguration().genotypeArgs.samplePloidy;
+        final int ploidy = localActiveGenotypingEngine.getGenotypeArgs().samplePloidy;
         final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy); // used to noCall all genotypes until the exact model is applied
 
         final Map<String, AlignmentContext> splitContexts;
@@ -688,7 +641,7 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
                 sample.getValue().getBasePileup().forEach(p -> PileupBasedAlleles.addMismatchPercentageToRead(p.getRead(), readsHeader, ref));
             }
             // The ploidy here is not dictated by the sample but by the simple genotyping-engine used to determine whether regions are active or not.
-            final int activeRegionDetectionHackishSamplePloidy = localActiveGenotypingEngine.getConfiguration().genotypeArgs.samplePloidy;
+            final int activeRegionDetectionHackishSamplePloidy = localActiveGenotypingEngine.getGenotypeArgs().samplePloidy;
             final double[] genotypeLikelihoods = ((RefVsAnyResult) referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(
                     activeRegionDetectionHackishSamplePloidy,
                     sample.getValue().getBasePileup(), ref.getBase(),
@@ -742,7 +695,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
 
         final List<VariantContext> VCpriors = new ArrayList<>();
         if (hcArgs.standardArgs.genotypeArgs.supportVariants != null) {
-            features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants).stream().forEach(VCpriors::add);
+            VCpriors.addAll(features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants));
         }
 
         if ( hcArgs.sampleNameToUse != null ) {
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
index 43b50fd2f9c..b12e48cee96 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
@@ -40,7 +40,7 @@
 /**
  * HaplotypeCaller's genotyping strategy implementation.
  */
-public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<StandardCallerArgumentCollection> {
+public class HaplotypeCallerGenotypingEngine extends GenotypingEngine {
 
     private static final Logger logger = LogManager.getLogger(HaplotypeCallerGenotypingEngine.class);
     private static final OneShotLogger DRAGENConaminationWarning = new OneShotLogger(logger);
@@ -150,7 +150,7 @@ public CalledHaplotypes assignGenotypeLikelihoods(final List<Haplotype> haplotyp
         // Walk along each position in the key set and create each event to be outputted
         final Set<Haplotype> calledHaplotypes = new HashSet<>();
         final List<VariantContext> returnCalls = new ArrayList<>();
-        final int ploidy = configuration.genotypeArgs.samplePloidy;
+        final int ploidy = getGenotypeArgs().samplePloidy;
         final List<Allele> noCallAlleles = GATKVariantContextUtils.noCallAlleles(ploidy);
 
         if (withBamOut) {
@@ -198,7 +198,7 @@ public CalledHaplotypes assignGenotypeLikelihoods(final List<Haplotype> haplotyp
 
             readAlleleLikelihoods.setVariantCallingSubsetUsed(variantCallingRelevantOverlap);
 
-            if (configuration.isSampleContaminationPresent()) {
+            if (getConfiguration().isSampleContaminationPresent()) {
                 // This warrants future evaluation as to the best way to handle disqualified reads
                 if (hcArgs.applyBQD || hcArgs.applyFRD) {
                     DRAGENConaminationWarning.warn("\\n=============================================================================" +
@@ -206,7 +206,7 @@ public CalledHaplotypes assignGenotypeLikelihoods(final List<Haplotype> haplotyp
                             "\n=============================================================================");
                 }
 
-                readAlleleLikelihoods.contaminationDownsampling(configuration.getSampleContamination());
+                readAlleleLikelihoods.contaminationDownsampling(getConfiguration().getSampleContamination());
             }
 
             if (HaplotypeCallerGenotypingDebugger.isEnabled()) {
@@ -595,7 +595,7 @@ private AlleleLikelihoods<GATKRead, Allele> prepareReadAlleleLikelihoodsForAnnot
         // We can reuse for annotation the likelihood for genotyping as long as there is no contamination filtering
         // or the user want to use the contamination filtered set for annotations.
         // Otherwise (else part) we need to do it again.
-        if (hcArgs.useFilteredReadMapForAnnotations || !configuration.isSampleContaminationPresent()) {
+        if (hcArgs.useFilteredReadMapForAnnotations || !getConfiguration().isSampleContaminationPresent()) {
             readAlleleLikelihoodsForAnnotations = readAlleleLikelihoodsForGenotyping;
             // the input likelihoods are supposed to have been filtered to only overlapping reads so no need to
             // do it again.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java
new file mode 100644
index 00000000000..1217b21fd9b
--- /dev/null
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java
@@ -0,0 +1,73 @@
+package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
+
+import htsjdk.samtools.util.Locatable;
+import htsjdk.samtools.util.OverlapDetector;
+import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine;
+import org.broadinstitute.hellbender.utils.Utils;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.function.IntFunction;
+
+/**
+ * A class which holds a cache of GenotypingEngines for handling different ploidies
+ * It is lazily initialized so GenotypingEngines are only created on as needed.
+ * @param <T> the GenotypingEngine implementation this provides
+ */
+public final class MultiPloidyGenotyperCache<T extends GenotypingEngine> {
+    private final Map<Integer, T> ploidyToGenotyperMap;
+    private final IntFunction<T> ploidyToGenotyper;
+    private final OverlapDetector<SimpleCount> ploidyRegions;
+    private final int defaultPloidy;
+
+
+    /**
+     * Create a new genotyper cache
+     * @param ploidyToGenotyper a function to generate a new GenotypingEngine given a ploidy
+     * @param defaultPloidy the default ploidy value
+     * @param alternatePloidyRegions a set of regions with alternate ploidys
+     */
+    public MultiPloidyGenotyperCache(IntFunction<T> ploidyToGenotyper, int defaultPloidy, OverlapDetector<SimpleCount> alternatePloidyRegions){
+        this.ploidyRegions = Utils.nonNull(alternatePloidyRegions);
+        this.ploidyToGenotyper = Utils.nonNull(ploidyToGenotyper);
+        this.defaultPloidy = defaultPloidy;
+        this.ploidyToGenotyperMap = new LinkedHashMap<>();
+    }
+
+    /**
+     * Determines the appropriate ploidy to use at given site for different genotyping engines.
+     * @param region Current region of interest
+     * @return if the region overlaps with one or more of the alternate ploidy regions, return the highest alternate ploidy
+     * otherwise return the default ploidy
+     */
+   private int getPloidyToUseAtThisSite(Locatable region) {
+       return ploidyRegions.getOverlaps(region)
+               .stream()
+               .mapToInt(SimpleCount::getCount)
+               .max()
+               .orElse(defaultPloidy);
+   }
+
+    /**
+     *
+     * @return the default genotyper that is configured for the default ploidy
+     */
+    public T getDefaultGenotypingEngine(){
+        return getCached(defaultPloidy);
+    }
+
+    /**
+     * get an appropriate GenotypingEngine for the given region.
+     * @param region the region to be genotyped
+     * @return a GenotypingEngine configured for the highest ploidy in the region given
+     */
+    public T getGenotypingEngine(final Locatable region) {
+        final int currentPloidy = getPloidyToUseAtThisSite(region);
+        return getCached(currentPloidy);
+    }
+
+    private T getCached(final int currentPloidy) {
+        return ploidyToGenotyperMap.computeIfAbsent(currentPloidy, ploidyToGenotyper::apply);
+    }
+}
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java
index 714faecb01b..afe4d880976 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java
@@ -102,7 +102,7 @@ public void testFinalizeAnnotationAgainstExpected(List<VariantContext> VCs, Vari
         VariantAnnotatorEngine annotatorEngine = new VariantAnnotatorEngine(getAnnotationsToUse(), null, Collections.emptyList(), false, false);
         final StandardCallerArgumentCollection standardArgs = new StandardCallerArgumentCollection();
 
-        GenotypingEngine<?> genotypingEngine = new MinimalGenotypingEngine(standardArgs, new IndexedSampleList(result.getSampleNamesOrderedByName()));
+        GenotypingEngine genotypingEngine = new MinimalGenotypingEngine(standardArgs, new IndexedSampleList(result.getSampleNamesOrderedByName()));
         genotypingEngine.setAnnotationEngine(annotatorEngine);
         VariantContext withGenotypes = genotypingEngine.calculateGenotypes(result);
         withGenotypes = new VariantContextBuilder(withGenotypes).attributes(result.getAttributes()).make();
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java
index beca5ddfb10..188987cf441 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java
@@ -29,7 +29,7 @@ public class GenotypingEngineUnitTest extends GATKBaseTest {
     private static final List<Allele> gtAlleles = GATKVariantContextUtils.noCallAlleles(2);
     private static final SampleList SAMPLES = new IndexedSampleList("test");
 
-    private GenotypingEngine<?> genotypingEngine;
+    private GenotypingEngine genotypingEngine;
     private static final Allele refA = Allele.create("A", true);
 
     @BeforeTest
@@ -41,7 +41,7 @@ public void init() {
         genotypingEngine.recordDeletions(deletionVC, Collections.singletonList(altT));
     }
 
-    private static GenotypingEngine<?> getGenotypingEngine() {
+    private static GenotypingEngine getGenotypingEngine() {
         final GenotypeCalculationArgumentCollection genotypeArgs = new GenotypeCalculationArgumentCollection();
         final StandardCallerArgumentCollection standardArgs = new StandardCallerArgumentCollection();
         return new MinimalGenotypingEngine(standardArgs, SAMPLES);
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 4770e8536bd..893739583ea 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -1,3 +1,4 @@
+
 package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
 
 import com.google.common.collect.ImmutableMap;
@@ -1219,15 +1220,15 @@ public Object[][] getContaminationCorrectionTestData() {
         // GATK 4 calls on the uncontaminated bam
         // GATK 3 calls on the contaminated bam with contamination correction
         return new Object[][] {
-                { contaminatedBam15Percent,
-                  0.15,
-                  contaminationFile,
-                  traversalInterval,
-                  b37_reference_20_21,
-                  false, // VCF mode
-                  expectedGATK4UncontaminatedCallsVCF,
-                  expectedGATK3ContaminationCorrectedCallsVCF
-                },
+//                { contaminatedBam15Percent,
+//                  0.15,
+//                  contaminationFile,
+//                  traversalInterval,
+//                  b37_reference_20_21,
+//                  false, // VCF mode
+//                  expectedGATK4UncontaminatedCallsVCF,
+//                  expectedGATK3ContaminationCorrectedCallsVCF
+//                },
                 { contaminatedBam15Percent,
                   0.15,
                   contaminationFile,
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java
new file mode 100644
index 00000000000..716c6e00780
--- /dev/null
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java
@@ -0,0 +1,82 @@
+package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
+
+import htsjdk.samtools.util.OverlapDetector;
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection;
+import org.broadinstitute.hellbender.utils.SimpleInterval;
+import org.broadinstitute.hellbender.utils.genotyper.SampleList;
+import org.jetbrains.annotations.NotNull;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.testng.Assert.*;
+
+public class MultiPloidyGenotyperCacheUnitTest extends GATKBaseTest {
+
+
+    @DataProvider
+    public static Object[][] getGenotyperParams() {
+        return new Object[][]{
+                {"1:10-30", 2},
+                {"1:70-85", 3},
+                {"1:80-93", 3},
+                {"1:89-92", 1}, //note that the explicitly set ploidy of 1 overrides the default ploidy 2 here
+                {"1:90-95", 1},
+                {"1:85-120", 5},
+                {"2:200", 2},
+                {"2:1-500", 4}
+        };
+    }
+
+    @Test(dataProvider = "getGenotyperParams")
+    public void testGettingGenotypers(String interval, int expectedPloidy){
+        final var detector = getOverlapDetector();
+        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
+        final MinimalGenotypingEngine genotypingEngine = genotypingCache.getGenotypingEngine(new SimpleInterval(interval));
+        Assert.assertEquals(genotypingEngine.getGenotypeArgs().samplePloidy, expectedPloidy);
+    }
+
+    @NotNull
+    private OverlapDetector<SimpleCount> getOverlapDetector() {
+        final var counts = List.of(
+                getCount("1:80", 3),
+                getCount("1:90-95", 1),
+                getCount("1:100-110", 5),
+                getCount("2:85-90", 4));
+        return OverlapDetector.create(counts);
+    }
+
+    @Test
+    public void testReturnsTheSameGenotyper(){
+        final var detector = getOverlapDetector();
+        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
+        final MinimalGenotypingEngine genotypingEngine = genotypingCache.getGenotypingEngine(new SimpleInterval("1:10-20"));
+        final MinimalGenotypingEngine genotypingEngine2 = genotypingCache.getGenotypingEngine(new SimpleInterval("2:10-20"));
+        Assert.assertSame(genotypingEngine, genotypingEngine2);
+    }
+
+    @Test
+    public void testGetDefaultBeforeInit() {
+        final var detector = getOverlapDetector();
+        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
+        Assert.assertNotNull(genotypingCache.getDefaultGenotypingEngine());
+    }
+
+    private MinimalGenotypingEngine getEngine(int ploidy){
+        final var args = new StandardCallerArgumentCollection();
+        args.genotypeArgs.samplePloidy = ploidy;
+        final var samples = SampleList.singletonSampleList("sample1");
+        return new MinimalGenotypingEngine(args, samples);
+    }
+
+    private static SimpleCount getCount(String location, int count){
+        return new SimpleCount(new SimpleInterval(location), count);
+    }
+
+}
\ No newline at end of file

From d9f77622d62e15f25e0fe33dc8b2bbf37d4f1d8d Mon Sep 17 00:00:00 2001
From: rickymagner <81349869+rickymagner@users.noreply.github.com>
Date: Thu, 7 Dec 2023 12:27:02 -0500
Subject: [PATCH 3/5] Update copy method and test

Remove old fields from HCE

Change data source to FeatureInput

Remove old commented code; add test arg copy sync deeper fields
---
 .../HaplotypeCallerArgumentCollection.java     | 18 +++++-------------
 .../haplotypecaller/HaplotypeCallerEngine.java | 16 +++-------------
 .../HaplotypeCallerIntegrationTest.java        | 16 +++++++++-------
 3 files changed, 17 insertions(+), 33 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
index 4ba22493c03..f818659bb5e 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
@@ -4,6 +4,7 @@
 import htsjdk.variant.variantcontext.VariantContext;
 import org.apache.arrow.util.VisibleForTesting;
 import org.apache.commons.lang3.ArrayUtils;
+import org.apache.commons.lang3.SerializationUtils;
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
@@ -67,7 +68,7 @@ protected ReadThreadingAssemblerArgumentCollection getReadThreadingAssemblerArgu
     }
 
     @Argument(fullName = PLOIDY_REGIONS_NAME, shortName = PLOIDY_REGIONS_NAME, doc = "Interval file with column specifying desired ploidy for genotyping models. Overrides default ploidy and user-provided --ploidy argument in specific regions.", optional = true)
-    public FeatureDataSource<NamedFeature> ploidyRegions = null;
+    public FeatureInput<NamedFeature> ploidyRegions = null;
 
     /**
      * You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This
@@ -320,20 +321,11 @@ boolean isFlowBasedCallingMode() {
         return flowMode != FlowMode.NONE;
     }
 
-    // Default constructor
-    public HaplotypeCallerArgumentCollection() {
-        super();
-    }
-
-    // Private constructor for use in copyWithNewPloidy
-    // Allows you to make new instances of hcArgs with identical fields except for genotyper ploidy
-    private HaplotypeCallerArgumentCollection(int ploidy) {
-        this.standardArgs.genotypeArgs.samplePloidy = ploidy;
-    }
-
     // Copy method used to create new hcArgs with same fields except input ploidy model
     public HaplotypeCallerArgumentCollection copyWithNewPloidy(int ploidy) {
-        return new HaplotypeCallerArgumentCollection(ploidy);
+        HaplotypeCallerArgumentCollection newArgsWithNewPloidy = SerializationUtils.clone(this);
+        newArgsWithNewPloidy.standardArgs.genotypeArgs.samplePloidy = ploidy;
+        return newArgsWithNewPloidy;
     }
 
     /**
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
index c2262272aaa..188b97a2d2e 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
@@ -6,6 +6,7 @@
 import htsjdk.samtools.util.Locatable;
 import htsjdk.samtools.util.OverlapDetector;
 import htsjdk.samtools.util.RuntimeIOException;
+import htsjdk.tribble.NamedFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
@@ -97,12 +98,6 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
      */
     protected final OverlapDetector<SimpleCount> ploidyRegionsOverlapDetector;
 
-    /**
-     * Map of user-provided ploidy values to corresponding active region genotyper. Values are checked as valid Integers during
-     * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
-     */
-    private final HashMap<Integer, MinimalGenotypingEngine> ploidyToActiveEvaluationGenotyper = new HashMap<>();
-
     protected ReadThreadingAssembler assemblyEngine = null;
 
     protected ReadLikelihoodCalculationEngine likelihoodCalculationEngine = null;
@@ -110,12 +105,6 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
     // If we are in PDHMM mode we need to hold onto two likelihoods engines for the fallback
     private ReadLikelihoodCalculationEngine pdhmmLikelihoodCalculationEngine = null;
 
-    /**
-     * Map of user-provided ploidy values to corresponding genotyper. Values are checked as valid Integers during
-     * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
-     */
-    protected final HashMap<Integer, HaplotypeCallerGenotypingEngine> ploidyToGenotyperMap = new HashMap<>();
-
     private VariantAnnotatorEngine annotationEngine = null;
 
     // fasta reference reader to supplement the edges of the reference sequence
@@ -221,7 +210,8 @@ public HaplotypeCallerEngine(final HaplotypeCallerArgumentCollection hcArgs, Ass
 
         // Parse the user provided custom ploidy regions into ploidyRegions object containing SimpleCounts
         if (this.hcArgs.ploidyRegions != null) {
-            this.hcArgs.ploidyRegions.forEach(r -> this.ploidyRegions.add(new SimpleCount(r)));
+            FeatureDataSource<NamedFeature> ploidyDataSource = new FeatureDataSource<>(this.hcArgs.ploidyRegions, FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES, NamedFeature.class);
+            ploidyDataSource.forEach(r -> this.ploidyRegions.add(new SimpleCount(r)));
         }
 
         for (SimpleCount region : this.ploidyRegions) {
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 893739583ea..543ff6776e3 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -1049,19 +1049,21 @@ public void testArgCollectionCopiesAreSynchronized() {
 
         HaplotypeCallerArgumentCollection hcArgs = new HaplotypeCallerArgumentCollection();
         hcArgs.applyBQD = !hcArgs.applyBQD;
-//        hcArgs.dontGenotype = !hcArgs.dontGenotype;
-//        hcArgs.standardArgs.annotateAllSitesWithPLs = !hcArgs.standardArgs.annotateAllSitesWithPLs;
+        hcArgs.dontGenotype = !hcArgs.dontGenotype;
+        hcArgs.standardArgs.annotateAllSitesWithPLs = !hcArgs.standardArgs.annotateAllSitesWithPLs;
+        hcArgs.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered = !hcArgs.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered;
 
         // Create copy with different ploidy and check tweaked values (and one control non-changed value) remain in sync
         HaplotypeCallerArgumentCollection hcArgsCopy = hcArgs.copyWithNewPloidy(3);
         Assert.assertEquals(hcArgs.applyBQD, hcArgsCopy.applyBQD);
-//        Assert.assertEquals(hcArgs.dontGenotype, hcArgsCopy.dontGenotype);
-//        Assert.assertEquals(hcArgs.standardArgs.annotateAllSitesWithPLs, hcArgsCopy.standardArgs.annotateAllSitesWithPLs);
-//        Assert.assertEquals(hcArgs.standardArgs.CONTAMINATION_FRACTION, hcArgs.standardArgs.CONTAMINATION_FRACTION);
+        Assert.assertEquals(hcArgs.dontGenotype, hcArgsCopy.dontGenotype);
+        Assert.assertEquals(hcArgs.standardArgs.annotateAllSitesWithPLs, hcArgsCopy.standardArgs.annotateAllSitesWithPLs);
+        Assert.assertEquals(hcArgs.standardArgs.CONTAMINATION_FRACTION, hcArgsCopy.standardArgs.CONTAMINATION_FRACTION);
+        Assert.assertEquals(hcArgs.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered, hcArgsCopy.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered);
 
         // Modify other values of copy and check they are now distinct, i.e. a "deep copy" was created above
-//        hcArgsCopy.applyBQD = !hcArgsCopy.applyBQD;
-//        Assert.assertNotEquals(hcArgs.applyBQD, hcArgsCopy.applyBQD);
+        hcArgsCopy.applyBQD = !hcArgsCopy.applyBQD;
+        Assert.assertNotEquals(hcArgs.applyBQD, hcArgsCopy.applyBQD);
     }
 
     // test that ReadFilterLibrary.NON_ZERO_REFERENCE_LENGTH_ALIGNMENT removes reads that consume zero reference bases

From a99eae2c981c4f840bb87c33822854589e6130e4 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Fri, 8 Dec 2023 14:23:20 -0500
Subject: [PATCH 4/5] Revert "Extracted a cache of Genotypers indexed by ploidy
 (#8598)"

This reverts commit a40ba3e7f9bcbdbc6dbf932cb15bd42236b73d65.
---
 .../tools/walkers/GenotypeGVCFsEngine.java    |   4 +-
 ...GenotypeCalculationArgumentCollection.java |   2 +-
 .../walkers/genotyper/GenotypingEngine.java   |  65 +++++----
 .../genotyper/MinimalGenotypingEngine.java    |  10 +-
 .../StandardCallerArgumentCollection.java     |   5 +-
 .../haplotypecaller/AlleleFilteringHC.java    |   2 +-
 .../HaplotypeCallerEngine.java                | 132 +++++++++++++-----
 .../HaplotypeCallerGenotypingEngine.java      |  10 +-
 .../MultiPloidyGenotyperCache.java            |  73 ----------
 .../ReducibleAnnotationBaseTest.java          |   2 +-
 .../genotyper/GenotypingEngineUnitTest.java   |   4 +-
 .../HaplotypeCallerIntegrationTest.java       |  19 ++-
 .../MultiPloidyGenotyperCacheUnitTest.java    |  82 -----------
 13 files changed, 157 insertions(+), 253 deletions(-)
 delete mode 100644 src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java
 delete mode 100644 src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
index f7f5f0ba9ef..312a90872e7 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
@@ -45,7 +45,7 @@ public class GenotypeGVCFsEngine
     private VariantAnnotatorEngine annotationEngine = null;
 
     //the genotyping engine
-    private GenotypingEngine forceOutputGenotypingEngine = null;
+    private GenotypingEngine<?> forceOutputGenotypingEngine = null;
     private MinimalGenotypingEngine genotypingEngine = null;
 
     // the INFO field annotation key names to remove
@@ -303,7 +303,7 @@ private VariantContext callSomaticGenotypes(final VariantContext vc, double tlod
         final VariantContextBuilder builder = new VariantContextBuilder(vc);
         final VariantContext regenotypedVC = builder.genotypes(newGenotypes).make();
 
-        final int maxAltAlleles = genotypingEngine.getGenotypeArgs().maxAlternateAlleles;
+        final int maxAltAlleles = genotypingEngine.getConfiguration().genotypeArgs.maxAlternateAlleles;
         List<Allele> allelesToKeep;
 
         //we need to make sure all alleles pass the tlodThreshold
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
index 75ba3d7784f..5090a87c484 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
@@ -71,7 +71,7 @@ public GenotypeCalculationArgumentCollection clone() {
      * Using this argument instructs the genotyper to annotate (in the INFO field) the number of alternate alleles that were originally discovered at the site.
      */
     @Argument(fullName = "annotate-with-num-discovered-alleles", doc = "If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site", optional = true)
-    public boolean annotateNumberOfAllelesDiscovered = false;
+    public boolean ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = false;
 
     /**
      * The expected heterozygosity value used to compute prior probability that a locus is non-reference.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
index 3121b71e873..1846fbe806d 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
@@ -28,13 +28,13 @@
 /**
  * Base class for genotyper engines.
  */
-public abstract class GenotypingEngine {
+public abstract class GenotypingEngine<Config extends StandardCallerArgumentCollection> {
 
     private final static int TOO_LONG_PL = 100000;
 
     protected final AlleleFrequencyCalculator alleleFrequencyCalculator;
 
-    private final StandardCallerArgumentCollection configuration;
+    protected final Config configuration;
 
     protected VariantAnnotatorEngine annotationEngine;
 
@@ -63,7 +63,7 @@ public abstract class GenotypingEngine {
      *
      * @throws IllegalArgumentException if any of {@code samples}, {@code configuration} is {@code null} or if {@code samples} is empty.
      */
-    protected GenotypingEngine(final StandardCallerArgumentCollection configuration,
+    protected GenotypingEngine(final Config configuration,
                                final SampleList samples,
                                final boolean doAlleleSpecificCalcs) {
         this.configuration = Utils.nonNull(configuration, "the configuration cannot be null");
@@ -89,16 +89,12 @@ public void setLogger(final Logger logger) {
 
     public Set<VCFInfoHeaderLine> getAppropriateVCFInfoHeaders() {
         final Set<VCFInfoHeaderLine> headerInfo = new LinkedHashSet<>();
-        if ( getGenotypeArgs().annotateNumberOfAllelesDiscovered) {
+        if ( configuration.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) {
             headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NUMBER_OF_DISCOVERED_ALLELES_KEY));
         }
         return headerInfo;
     }
 
-    public GenotypeCalculationArgumentCollection getGenotypeArgs() {
-        return getConfiguration().genotypeArgs;
-    }
-
     /**
      * Changes the annotation engine for this genotyping-engine.
      *
@@ -113,7 +109,7 @@ public void setAnnotationEngine(final VariantAnnotatorEngine annotationEngine) {
      *
      * @return never {@code null}.
      */
-    protected StandardCallerArgumentCollection getConfiguration() {
+    public Config getConfiguration() {
         return configuration;
     }
 
@@ -135,8 +131,8 @@ public VariantContext calculateGenotypes(final VariantContext vc, final Genotype
             return null;
         }
 
-        final int defaultPloidy = getGenotypeArgs().samplePloidy;
-        final int maxAltAlleles = getGenotypeArgs().maxAlternateAlleles;
+        final int defaultPloidy = configuration.genotypeArgs.samplePloidy;
+        final int maxAltAlleles = configuration.genotypeArgs.maxAlternateAlleles;
 
         VariantContext reducedVC = vc;
         if (maxAltAlleles < vc.getAlternateAlleles().size()) {
@@ -160,7 +156,7 @@ public VariantContext calculateGenotypes(final VariantContext vc, final Genotype
 
         // note the math.abs is necessary because -10 * 0.0 => -0.0 which isn't nice
         final double log10Confidence =
-                    !outputAlternativeAlleles.siteIsMonomorphic || getConfiguration().annotateAllSitesWithPLs
+                    !outputAlternativeAlleles.siteIsMonomorphic || configuration.annotateAllSitesWithPLs
                             ? AFresult.log10ProbOnlyRefAlleleExists() + 0.0 : AFresult.log10ProbVariantPresent() + 0.0;
 
         // Add 0.0 removes -0.0 occurrences.
@@ -192,11 +188,11 @@ && noAllelesOrFirstAlleleIsNotNonRef(outputAlternativeAlleles.alleles) && forced
         // create the genotypes
         //TODO: omit subsetting if output alleles is not a proper subset of vc.getAlleles
         final GenotypesContext genotypes = outputAlleles.size() == 1 ? GATKVariantContextUtils.subsetToRefOnly(vc, defaultPloidy) :
-                AlleleSubsettingUtils.subsetAlleles(vc.getGenotypes(), defaultPloidy, vc.getAlleles(), outputAlleles, gpc, getGenotypeArgs().genotypeAssignmentMethod);
+                AlleleSubsettingUtils.subsetAlleles(vc.getGenotypes(), defaultPloidy, vc.getAlleles(), outputAlleles, gpc, configuration.genotypeArgs.genotypeAssignmentMethod);
 
-        if (getGenotypeArgs().usePosteriorProbabilitiesToCalculateQual && hasPosteriors(genotypes)) {
+        if (configuration.genotypeArgs.usePosteriorProbabilitiesToCalculateQual && hasPosteriors(genotypes)) {
             final double log10NoVariantPosterior = phredNoVariantPosteriorProbability(outputAlleles, genotypes) * -.1;
-            final double qualUpdate = !outputAlternativeAlleles.siteIsMonomorphic || getConfiguration().annotateAllSitesWithPLs
+            final double qualUpdate = !outputAlternativeAlleles.siteIsMonomorphic || configuration.annotateAllSitesWithPLs
                     ? log10NoVariantPosterior + 0.0 : MathUtils.log10OneMinusPow10(log10NoVariantPosterior) + 0.0;
             if (!Double.isNaN(qualUpdate)) {
                 builder.log10PError(qualUpdate);
@@ -264,23 +260,30 @@ static boolean noAllelesOrFirstAlleleIsNotNonRef(List<Allele> altAlleles) {
     protected abstract String callSourceString();
 
     /**
-         * Holds information about the alternative allele subsetting based on supporting evidence, genotyping and
-         * output modes.
-         */
-        private record OutputAlleleSubset(List<Allele> alleles, List<Integer> mleCounts, boolean siteIsMonomorphic) {
-        private OutputAlleleSubset {
+     * Holds information about the alternative allele subsetting based on supporting evidence, genotyping and
+     * output modes.
+     */
+    private static class OutputAlleleSubset {
+        private  final List<Allele> alleles;
+        private  final boolean siteIsMonomorphic;
+        private  final List<Integer> mleCounts;
+
+        private OutputAlleleSubset(final List<Allele> alleles, final List<Integer> mleCounts, final boolean siteIsMonomorphic) {
             Utils.nonNull(alleles, "alleles");
             Utils.nonNull(mleCounts, "mleCounts");
+            this.siteIsMonomorphic = siteIsMonomorphic;
+            this.alleles = alleles;
+            this.mleCounts = mleCounts;
         }
 
-            private List<Allele> outputAlleles(final Allele referenceAllele) {
-                return Stream.concat(Stream.of(referenceAllele), alleles.stream()).collect(Collectors.toList());
-            }
+        private List<Allele> outputAlleles(final Allele referenceAllele) {
+            return Stream.concat(Stream.of(referenceAllele), alleles.stream()).collect(Collectors.toList());
+        }
 
-            public List<Integer> alternativeAlleleMLECounts() {
-                return mleCounts;
-            }
+        public List<Integer> alternativeAlleleMLECounts() {
+            return mleCounts;
         }
+    }
 
 
     /**
@@ -305,7 +308,7 @@ private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalculationResult
                 // we want to keep the NON_REF symbolic allele but only in the absence of a non-symbolic allele, e.g.
                 // if we combined a ref / NON_REF gVCF with a ref / alt gVCF
                 final boolean isNonRefWhichIsLoneAltAllele = alternativeAlleleCount == 1 && allele.equals(Allele.NON_REF_ALLELE);
-                final boolean isPlausible = afCalculationResult.passesThreshold(allele, getGenotypeArgs().standardConfidenceForCalling);
+                final boolean isPlausible = afCalculationResult.passesThreshold(allele, configuration.genotypeArgs.standardConfidenceForCalling);
 
                 //it's possible that the upstream deletion that spanned this site was not emitted, mooting the symbolic spanning deletion allele
                 final boolean isSpuriousSpanningDeletion = GATKVCFConstants.isSpanningDeletion(allele) && !isVcCoveredByDeletion(vc);
@@ -412,16 +415,16 @@ protected final boolean cannotBeGenotyped(final VariantContext vc) {
      * This does not necessarily emit calls for all sites in a region (see {@link OutputMode}).
      */
     protected boolean emitAllActiveSites() {
-        return getConfiguration().outputMode == OutputMode.EMIT_ALL_ACTIVE_SITES;
+        return configuration.outputMode == OutputMode.EMIT_ALL_ACTIVE_SITES;
     }
 
     protected final boolean passesEmitThreshold(final double conf, final boolean bestGuessIsRef) {
-        return (getConfiguration().outputMode == OutputMode.EMIT_ALL_CONFIDENT_SITES || !bestGuessIsRef) &&
+        return (configuration.outputMode == OutputMode.EMIT_ALL_CONFIDENT_SITES || !bestGuessIsRef) &&
                 passesCallThreshold(conf);
     }
 
     protected final boolean passesCallThreshold(final double conf) {
-        return conf >= getGenotypeArgs().standardConfidenceForCalling;
+        return conf >= configuration.genotypeArgs.standardConfidenceForCalling;
     }
 
     protected Map<String,Object> composeCallAttributes(final VariantContext vc, final List<Integer> alleleCountsofMLE,
@@ -454,7 +457,7 @@ protected Map<String,Object> composeCallAttributes(final VariantContext vc, fina
             attributes.put(GATKVCFConstants.AS_QUAL_KEY, perAlleleQuals.stream().mapToInt(q -> Math.round(q)).boxed().collect(Collectors.toList()));
         }
 
-        if ( getGenotypeArgs().annotateNumberOfAllelesDiscovered) {
+        if ( configuration.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) {
             attributes.put(GATKVCFConstants.NUMBER_OF_DISCOVERED_ALLELES_KEY, vc.getAlternateAlleles().size());
         }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java
index a72442bda9e..4d5b3986e91 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java
@@ -19,7 +19,7 @@
  * used only by the HaplotypeCaller for its isActive() determination. Should not be used for
  * any other purpose!
  */
-public final class MinimalGenotypingEngine extends GenotypingEngine {
+public final class MinimalGenotypingEngine extends GenotypingEngine<StandardCallerArgumentCollection> {
 
     private final DragstrParams dragstrParams;
 
@@ -61,7 +61,7 @@ public MinimalGenotypingEngine(final StandardCallerArgumentCollection configurat
 
     @Override
     protected boolean forceKeepAllele(final Allele allele) {
-        return getConfiguration().annotateAllSitesWithPLs;
+        return configuration.annotateAllSitesWithPLs;
     }
 
     @Override
@@ -71,8 +71,8 @@ protected String callSourceString() {
 
     @Override
     public VariantContext calculateGenotypes(final VariantContext vc) {
-        if (dragstrParams == null || getGenotypeArgs().dontUseDragstrPriors || !GATKVariantContextUtils.containsInlineIndel(vc) || referenceContext == null) {
-            final GenotypePriorCalculator gpc = GenotypePriorCalculator.assumingHW(getGenotypeArgs());
+        if (dragstrParams == null || getConfiguration().genotypeArgs.dontUseDragstrPriors || !GATKVariantContextUtils.containsInlineIndel(vc) || referenceContext == null) {
+            final GenotypePriorCalculator gpc = GenotypePriorCalculator.assumingHW(configuration.genotypeArgs);
             return calculateGenotypes(vc, gpc, Collections.emptyList());
         } else {
 
@@ -90,7 +90,7 @@ public VariantContext calculateGenotypes(final VariantContext vc) {
             final int period = analyzer.period(startOffset);
             final int repeats = analyzer.repeatLength(startOffset);
 
-            final GenotypePriorCalculator gpc = GenotypePriorCalculator.givenDragstrParams(dragstrParams, period, repeats, Math.log10(getGenotypeArgs().snpHeterozygosity), 2.0);
+            final GenotypePriorCalculator gpc = GenotypePriorCalculator.givenDragstrParams(dragstrParams, period, repeats, Math.log10(getConfiguration().genotypeArgs.snpHeterozygosity), 2.0);
             return  calculateGenotypes(vc, gpc, Collections.emptyList());
         }
     }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java
index 0ca6a19975e..a6b25ed7c53 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/StandardCallerArgumentCollection.java
@@ -2,7 +2,6 @@
 
 import htsjdk.variant.variantcontext.VariantContext;
 import org.apache.commons.collections4.map.DefaultedMap;
-import org.apache.commons.lang3.SerializationUtils;
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
@@ -18,7 +17,7 @@
 /**
  * This is pulled out so that every caller isn't exposed to the arguments from every other caller.
  */
-public final class StandardCallerArgumentCollection implements Serializable {
+public class StandardCallerArgumentCollection implements Serializable {
     private static final long serialVersionUID = 1L;
 
     /**
@@ -29,7 +28,7 @@ public final class StandardCallerArgumentCollection implements Serializable {
     public void copyStandardCallerArgsFrom( final StandardCallerArgumentCollection other ) {
         Utils.nonNull(other);
 
-        this.genotypeArgs = SerializationUtils.clone(other.genotypeArgs);
+        this.genotypeArgs = other.genotypeArgs.clone();
         this.CONTAMINATION_FRACTION = other.CONTAMINATION_FRACTION;
         this.CONTAMINATION_FRACTION_FILE = other.CONTAMINATION_FRACTION_FILE != null ? new File(other.CONTAMINATION_FRACTION_FILE.getAbsolutePath()) : null;
         if ( other.sampleContamination != null ) {
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
index 66b76159ae9..2788cc21575 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
@@ -29,7 +29,7 @@ public class AlleleFilteringHC extends AlleleFiltering {
     public AlleleFilteringHC(HaplotypeCallerArgumentCollection _hcargs, OutputStreamWriter assemblyDebugStream, HaplotypeCallerGenotypingEngine _genotypingEngine){
         super(_hcargs, assemblyDebugStream);
         genotypingEngine = _genotypingEngine;
-        GenotypeCalculationArgumentCollection config = genotypingEngine.getGenotypeArgs();
+        GenotypeCalculationArgumentCollection config = genotypingEngine.getConfiguration().genotypeArgs;
          afCalc = AlleleFrequencyCalculator.makeCalculator(config);
     }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
index 188b97a2d2e..9e09eeba8a9 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
@@ -26,6 +26,7 @@
 import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
 import org.broadinstitute.hellbender.tools.walkers.annotator.*;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection;
@@ -98,6 +99,22 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
      */
     protected final OverlapDetector<SimpleCount> ploidyRegionsOverlapDetector;
 
+    /**
+     * List of all custom ploidies provided by user
+     */
+    private final LinkedHashSet<Integer> allCustomPloidies;
+
+    /**
+     * The default genotyping engine for the isActive() determination
+     */
+    private MinimalGenotypingEngine defaultActiveRegionEvaluationGenotyperEngine = null;
+
+    /**
+     * Map of user-provided ploidy values to corresponding active region genotyper. Values are checked as valid Integers during
+     * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
+     */
+    private final HashMap<Integer, MinimalGenotypingEngine> ploidyToActiveEvaluationGenotyper = new HashMap<>();
+
     protected ReadThreadingAssembler assemblyEngine = null;
 
     protected ReadLikelihoodCalculationEngine likelihoodCalculationEngine = null;
@@ -105,6 +122,17 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
     // If we are in PDHMM mode we need to hold onto two likelihoods engines for the fallback
     private ReadLikelihoodCalculationEngine pdhmmLikelihoodCalculationEngine = null;
 
+    /**
+     * The default genotyping engine to use for actual variant calling and genotyping in an active region.
+     */
+    protected HaplotypeCallerGenotypingEngine defaultGenotypingEngine = null;
+
+    /**
+     * Map of user-provided ploidy values to corresponding genotyper. Values are checked as valid Integers during
+     * initialization, but Strings are used as keys to avoid parsing repeatedly during runtime.
+     */
+    protected final HashMap<Integer, HaplotypeCallerGenotypingEngine> ploidyToGenotyperMap = new HashMap<>();
+
     private VariantAnnotatorEngine annotationEngine = null;
 
     // fasta reference reader to supplement the edges of the reference sequence
@@ -169,8 +197,6 @@ public class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
 
     private static final Allele FAKE_REF_ALLELE = Allele.create("N", true); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file
     private static final Allele FAKE_ALT_ALLELE = Allele.create("<FAKE_ALT>", false); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file
-    private MultiPloidyGenotyperCache<HaplotypeCallerGenotypingEngine> genotypingEngines;
-    private MultiPloidyGenotyperCache<MinimalGenotypingEngine> activeRegionGenotypingEngines;
 
     /**
      * Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header,
@@ -216,11 +242,12 @@ public HaplotypeCallerEngine(final HaplotypeCallerArgumentCollection hcArgs, Ass
 
         for (SimpleCount region : this.ploidyRegions) {
             if (!IntervalUtils.intervalIsOnDictionaryContig(region.getInterval(), readsHeader.getSequenceDictionary())) {
-                throw new UserException("Invalid region provided for --" + HaplotypeCallerArgumentCollection.PLOIDY_REGIONS_NAME + " at " + region.getContig() + ":" + region.getStart() + "-" + region.getEnd() + ". Contig name or endpoint doesn't match read sequence dictionary.");
+                throw new UserException("Invalid region provided for --ploidy-regions at " + region.getContig() + ":" + region.getStart() + "-" + region.getEnd() + ". Contig name or endpoint doesn't match read sequence dictionary.");
             }
         }
 
         this.ploidyRegionsOverlapDetector = OverlapDetector.create(this.ploidyRegions);
+        this.allCustomPloidies = this.ploidyRegions.stream().map(SimpleCount::getCount).collect(Collectors.toCollection(LinkedHashSet::new));
 
         trimmer = new AssemblyRegionTrimmer(assemblyRegionArgs, readsHeader.getSequenceDictionary());
         initialize(createBamOutIndex, createBamOutMD5);
@@ -268,10 +295,16 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5
 
         initializeActiveRegionEvaluationGenotyperEngine();
 
-        final int defaultPloidy = hcArgs.standardArgs.genotypeArgs.samplePloidy;
-        genotypingEngines = new MultiPloidyGenotyperCache<>(this::makeGenotypingEngine,
-                defaultPloidy,
-                ploidyRegionsOverlapDetector);
+        defaultGenotypingEngine = new HaplotypeCallerGenotypingEngine(hcArgs, samplesList, ! hcArgs.doNotRunPhysicalPhasing, hcArgs.applyBQD);
+        defaultGenotypingEngine.setAnnotationEngine(annotationEngine);
+
+        // Create other custom genotyping engines if user provided ploidyRegions
+        for (final int ploidy : this.allCustomPloidies) {
+            HaplotypeCallerArgumentCollection newPloidyHcArgs = hcArgs.copyWithNewPloidy(ploidy);
+            HaplotypeCallerGenotypingEngine newGenotypingEngine = new HaplotypeCallerGenotypingEngine(newPloidyHcArgs, samplesList, ! hcArgs.doNotRunPhysicalPhasing, hcArgs.applyBQD);
+            newGenotypingEngine.setAnnotationEngine(annotationEngine);
+            this.ploidyToGenotyperMap.put(ploidy, newGenotypingEngine);
+        }
 
         boolean isFlowBased = (hcArgs.likelihoodArgs.likelihoodEngineImplementation == ReadLikelihoodCalculationEngine.Implementation.FlowBased)
                 || (hcArgs.likelihoodArgs.likelihoodEngineImplementation == ReadLikelihoodCalculationEngine.Implementation.FlowBasedHMM);
@@ -325,13 +358,6 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5
                 : null);
     }
 
-    private HaplotypeCallerGenotypingEngine makeGenotypingEngine(int ploidy) {
-        final HaplotypeCallerArgumentCollection newPloidyHcArgs = hcArgs.copyWithNewPloidy(ploidy);
-        final HaplotypeCallerGenotypingEngine newGenotypingEngine = new HaplotypeCallerGenotypingEngine(newPloidyHcArgs, samplesList, !newPloidyHcArgs.doNotRunPhysicalPhasing, newPloidyHcArgs.applyBQD);
-        newGenotypingEngine.setAnnotationEngine(annotationEngine);
-        return newGenotypingEngine;
-    }
-
     private boolean isVCFMode() {
         return hcArgs.emitReferenceConfidence == ReferenceConfidenceMode.NONE;
     }
@@ -407,28 +433,27 @@ private void initializeSamples() {
 
     private void initializeActiveRegionEvaluationGenotyperEngine() {
         final StandardCallerArgumentCollection activeRegionArgs = new StandardCallerArgumentCollection();
-
         activeRegionArgs.copyStandardCallerArgsFrom(hcArgs.standardArgs);
 
         activeRegionArgs.outputMode = OutputMode.EMIT_VARIANTS_ONLY;
         activeRegionArgs.genotypeArgs.standardConfidenceForCalling = Math.min(MAXMIN_CONFIDENCE_FOR_CONSIDERING_A_SITE_AS_POSSIBLE_VARIANT_IN_ACTIVE_REGION_DISCOVERY, hcArgs.standardArgs.genotypeArgs.standardConfidenceForCalling); // low values used for isActive determination only, default/user-specified values used for actual calling
         activeRegionArgs.CONTAMINATION_FRACTION = 0.0;
         activeRegionArgs.CONTAMINATION_FRACTION_FILE = null;
-
-        final int defaultPloidy = hcArgs.standardArgs.genotypeArgs.samplePloidy;
-        activeRegionGenotypingEngines = new MultiPloidyGenotyperCache<>(ploidy -> {
-                // Seems that at least with some test data we can lose genuine haploid variation if we use ploidy == 1
-                final int adjustedPloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, ploidy);
-                final StandardCallerArgumentCollection newPloidyActiveArgs = new StandardCallerArgumentCollection();
-                newPloidyActiveArgs.copyStandardCallerArgsFrom(activeRegionArgs);
-                newPloidyActiveArgs.genotypeArgs.samplePloidy = adjustedPloidy;
-                final MinimalGenotypingEngine genotyper = new MinimalGenotypingEngine(newPloidyActiveArgs, samplesList);
-                genotyper.setLogger(logger);
-                return genotyper;
-            },
-                defaultPloidy,
-                ploidyRegionsOverlapDetector
-        );
+        // Seems that at least with some test data we can lose genuine haploid variation if we use ploidy == 1
+        activeRegionArgs.genotypeArgs.samplePloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, hcArgs.standardArgs.genotypeArgs.samplePloidy);
+
+        defaultActiveRegionEvaluationGenotyperEngine = new MinimalGenotypingEngine(activeRegionArgs, samplesList);
+        defaultActiveRegionEvaluationGenotyperEngine.setLogger(logger);
+
+        // If custom ploidyRegions provided, create corresponding map for active region determination genotyper
+        for (final int ploidy : this.allCustomPloidies) {
+            StandardCallerArgumentCollection newPloidyActiveArgs = new StandardCallerArgumentCollection();
+            newPloidyActiveArgs.copyStandardCallerArgsFrom(activeRegionArgs);
+            newPloidyActiveArgs.genotypeArgs.samplePloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, ploidy);
+            MinimalGenotypingEngine newActiveGenotypingEngine = new MinimalGenotypingEngine(newPloidyActiveArgs, samplesList);
+            newActiveGenotypingEngine.setLogger(logger);
+            this.ploidyToActiveEvaluationGenotyper.put(ploidy, newActiveGenotypingEngine);
+        }
     }
 
     /**
@@ -501,7 +526,7 @@ public VCFHeader makeVCFHeader( final SAMSequenceDictionary sequenceDictionary,
         final Set<VCFHeaderLine> headerInfo = new HashSet<>();
         headerInfo.addAll(defaultToolHeaderLines);
 
-        headerInfo.addAll(genotypingEngines.getDefaultGenotypingEngine().getAppropriateVCFInfoHeaders());
+        headerInfo.addAll(defaultGenotypingEngine.getAppropriateVCFInfoHeaders());
         // all annotation fields from VariantAnnotatorEngine
         headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions(emitReferenceConfidence()));
         // all callers need to add these standard annotation header lines
@@ -569,13 +594,41 @@ public void writeHeader( final VariantContextWriter vcfWriter, final SAMSequence
         vcfWriter.writeHeader(makeVCFHeader(sequenceDictionary, defaultToolHeaderLines));
     }
 
+    /**
+     * Determines the appropriate ploidy to use at given site for different genotyping engines.
+     * @param region Current region of interest
+     * @return Ploidy value to use here given user inputs, or -1 if fall back to default
+     */
+    private int getPloidyToUseAtThisSite(Locatable region) {
+        Set<SimpleCount> overlaps = this.ploidyRegionsOverlapDetector.getOverlaps(region);
+        // Return first engine for interval overlapping this region
+        if (!overlaps.isEmpty()) {
+            Iterator<SimpleCount> intervals = overlaps.iterator();
+            int max = intervals.next().getCount();
+            while (intervals.hasNext()) {
+                int next = intervals.next().getCount();
+                if (next > max) {
+                    max = next;
+                }
+            }
+            return max;
+        } else {
+            return -1; // Sentinel value to fall back to default genotyper
+        }
+    }
+
     /**
      * Selects appropriate active region genotyping engine for given region
      * @param region Current region of interest
      * @return Active genotyping engine with correct ploidy setting for given region
      */
     private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
-        return activeRegionGenotypingEngines.getGenotypingEngine(region);
+        int currentPloidy = getPloidyToUseAtThisSite(region);
+        if (currentPloidy == -1) {
+            return this.defaultActiveRegionEvaluationGenotyperEngine;
+        } else {
+            return this.ploidyToActiveEvaluationGenotyper.get(currentPloidy);
+        }
     }
 
     /**
@@ -584,9 +637,14 @@ private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
      * @return Genotyping engine with correct ploidy setting for given region
      */
     protected HaplotypeCallerGenotypingEngine getLocalGenotypingEngine(Locatable region) {
-        return genotypingEngines.getGenotypingEngine(region);
+        int currentPloidy = getPloidyToUseAtThisSite(region);
+        if (currentPloidy == -1) {
+            return this.defaultGenotypingEngine;
+        } else {
+            return this.ploidyToGenotyperMap.get(currentPloidy);
+        }
     }
-    
+
     /**
      * Given a pileup, returns an ActivityProfileState containing the probability (0.0 to 1.0) that it's an "active" site.
      *
@@ -612,7 +670,7 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
             return new ActivityProfileState(ref.getInterval(), 0.0);
         }
 
-        final int ploidy = localActiveGenotypingEngine.getGenotypeArgs().samplePloidy;
+        final int ploidy = localActiveGenotypingEngine.getConfiguration().genotypeArgs.samplePloidy;
         final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy); // used to noCall all genotypes until the exact model is applied
 
         final Map<String, AlignmentContext> splitContexts;
@@ -631,7 +689,7 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
                 sample.getValue().getBasePileup().forEach(p -> PileupBasedAlleles.addMismatchPercentageToRead(p.getRead(), readsHeader, ref));
             }
             // The ploidy here is not dictated by the sample but by the simple genotyping-engine used to determine whether regions are active or not.
-            final int activeRegionDetectionHackishSamplePloidy = localActiveGenotypingEngine.getGenotypeArgs().samplePloidy;
+            final int activeRegionDetectionHackishSamplePloidy = localActiveGenotypingEngine.getConfiguration().genotypeArgs.samplePloidy;
             final double[] genotypeLikelihoods = ((RefVsAnyResult) referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(
                     activeRegionDetectionHackishSamplePloidy,
                     sample.getValue().getBasePileup(), ref.getBase(),
@@ -685,7 +743,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
 
         final List<VariantContext> VCpriors = new ArrayList<>();
         if (hcArgs.standardArgs.genotypeArgs.supportVariants != null) {
-            VCpriors.addAll(features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants));
+            features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants).stream().forEach(VCpriors::add);
         }
 
         if ( hcArgs.sampleNameToUse != null ) {
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
index b12e48cee96..43b50fd2f9c 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
@@ -40,7 +40,7 @@
 /**
  * HaplotypeCaller's genotyping strategy implementation.
  */
-public class HaplotypeCallerGenotypingEngine extends GenotypingEngine {
+public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<StandardCallerArgumentCollection> {
 
     private static final Logger logger = LogManager.getLogger(HaplotypeCallerGenotypingEngine.class);
     private static final OneShotLogger DRAGENConaminationWarning = new OneShotLogger(logger);
@@ -150,7 +150,7 @@ public CalledHaplotypes assignGenotypeLikelihoods(final List<Haplotype> haplotyp
         // Walk along each position in the key set and create each event to be outputted
         final Set<Haplotype> calledHaplotypes = new HashSet<>();
         final List<VariantContext> returnCalls = new ArrayList<>();
-        final int ploidy = getGenotypeArgs().samplePloidy;
+        final int ploidy = configuration.genotypeArgs.samplePloidy;
         final List<Allele> noCallAlleles = GATKVariantContextUtils.noCallAlleles(ploidy);
 
         if (withBamOut) {
@@ -198,7 +198,7 @@ public CalledHaplotypes assignGenotypeLikelihoods(final List<Haplotype> haplotyp
 
             readAlleleLikelihoods.setVariantCallingSubsetUsed(variantCallingRelevantOverlap);
 
-            if (getConfiguration().isSampleContaminationPresent()) {
+            if (configuration.isSampleContaminationPresent()) {
                 // This warrants future evaluation as to the best way to handle disqualified reads
                 if (hcArgs.applyBQD || hcArgs.applyFRD) {
                     DRAGENConaminationWarning.warn("\\n=============================================================================" +
@@ -206,7 +206,7 @@ public CalledHaplotypes assignGenotypeLikelihoods(final List<Haplotype> haplotyp
                             "\n=============================================================================");
                 }
 
-                readAlleleLikelihoods.contaminationDownsampling(getConfiguration().getSampleContamination());
+                readAlleleLikelihoods.contaminationDownsampling(configuration.getSampleContamination());
             }
 
             if (HaplotypeCallerGenotypingDebugger.isEnabled()) {
@@ -595,7 +595,7 @@ private AlleleLikelihoods<GATKRead, Allele> prepareReadAlleleLikelihoodsForAnnot
         // We can reuse for annotation the likelihood for genotyping as long as there is no contamination filtering
         // or the user want to use the contamination filtered set for annotations.
         // Otherwise (else part) we need to do it again.
-        if (hcArgs.useFilteredReadMapForAnnotations || !getConfiguration().isSampleContaminationPresent()) {
+        if (hcArgs.useFilteredReadMapForAnnotations || !configuration.isSampleContaminationPresent()) {
             readAlleleLikelihoodsForAnnotations = readAlleleLikelihoodsForGenotyping;
             // the input likelihoods are supposed to have been filtered to only overlapping reads so no need to
             // do it again.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java
deleted file mode 100644
index 1217b21fd9b..00000000000
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCache.java
+++ /dev/null
@@ -1,73 +0,0 @@
-package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
-
-import htsjdk.samtools.util.Locatable;
-import htsjdk.samtools.util.OverlapDetector;
-import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
-import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine;
-import org.broadinstitute.hellbender.utils.Utils;
-
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.function.IntFunction;
-
-/**
- * A class which holds a cache of GenotypingEngines for handling different ploidies
- * It is lazily initialized so GenotypingEngines are only created on as needed.
- * @param <T> the GenotypingEngine implementation this provides
- */
-public final class MultiPloidyGenotyperCache<T extends GenotypingEngine> {
-    private final Map<Integer, T> ploidyToGenotyperMap;
-    private final IntFunction<T> ploidyToGenotyper;
-    private final OverlapDetector<SimpleCount> ploidyRegions;
-    private final int defaultPloidy;
-
-
-    /**
-     * Create a new genotyper cache
-     * @param ploidyToGenotyper a function to generate a new GenotypingEngine given a ploidy
-     * @param defaultPloidy the default ploidy value
-     * @param alternatePloidyRegions a set of regions with alternate ploidys
-     */
-    public MultiPloidyGenotyperCache(IntFunction<T> ploidyToGenotyper, int defaultPloidy, OverlapDetector<SimpleCount> alternatePloidyRegions){
-        this.ploidyRegions = Utils.nonNull(alternatePloidyRegions);
-        this.ploidyToGenotyper = Utils.nonNull(ploidyToGenotyper);
-        this.defaultPloidy = defaultPloidy;
-        this.ploidyToGenotyperMap = new LinkedHashMap<>();
-    }
-
-    /**
-     * Determines the appropriate ploidy to use at given site for different genotyping engines.
-     * @param region Current region of interest
-     * @return if the region overlaps with one or more of the alternate ploidy regions, return the highest alternate ploidy
-     * otherwise return the default ploidy
-     */
-   private int getPloidyToUseAtThisSite(Locatable region) {
-       return ploidyRegions.getOverlaps(region)
-               .stream()
-               .mapToInt(SimpleCount::getCount)
-               .max()
-               .orElse(defaultPloidy);
-   }
-
-    /**
-     *
-     * @return the default genotyper that is configured for the default ploidy
-     */
-    public T getDefaultGenotypingEngine(){
-        return getCached(defaultPloidy);
-    }
-
-    /**
-     * get an appropriate GenotypingEngine for the given region.
-     * @param region the region to be genotyped
-     * @return a GenotypingEngine configured for the highest ploidy in the region given
-     */
-    public T getGenotypingEngine(final Locatable region) {
-        final int currentPloidy = getPloidyToUseAtThisSite(region);
-        return getCached(currentPloidy);
-    }
-
-    private T getCached(final int currentPloidy) {
-        return ploidyToGenotyperMap.computeIfAbsent(currentPloidy, ploidyToGenotyper::apply);
-    }
-}
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java
index afe4d880976..714faecb01b 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java
@@ -102,7 +102,7 @@ public void testFinalizeAnnotationAgainstExpected(List<VariantContext> VCs, Vari
         VariantAnnotatorEngine annotatorEngine = new VariantAnnotatorEngine(getAnnotationsToUse(), null, Collections.emptyList(), false, false);
         final StandardCallerArgumentCollection standardArgs = new StandardCallerArgumentCollection();
 
-        GenotypingEngine genotypingEngine = new MinimalGenotypingEngine(standardArgs, new IndexedSampleList(result.getSampleNamesOrderedByName()));
+        GenotypingEngine<?> genotypingEngine = new MinimalGenotypingEngine(standardArgs, new IndexedSampleList(result.getSampleNamesOrderedByName()));
         genotypingEngine.setAnnotationEngine(annotatorEngine);
         VariantContext withGenotypes = genotypingEngine.calculateGenotypes(result);
         withGenotypes = new VariantContextBuilder(withGenotypes).attributes(result.getAttributes()).make();
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java
index 188987cf441..beca5ddfb10 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java
@@ -29,7 +29,7 @@ public class GenotypingEngineUnitTest extends GATKBaseTest {
     private static final List<Allele> gtAlleles = GATKVariantContextUtils.noCallAlleles(2);
     private static final SampleList SAMPLES = new IndexedSampleList("test");
 
-    private GenotypingEngine genotypingEngine;
+    private GenotypingEngine<?> genotypingEngine;
     private static final Allele refA = Allele.create("A", true);
 
     @BeforeTest
@@ -41,7 +41,7 @@ public void init() {
         genotypingEngine.recordDeletions(deletionVC, Collections.singletonList(altT));
     }
 
-    private static GenotypingEngine getGenotypingEngine() {
+    private static GenotypingEngine<?> getGenotypingEngine() {
         final GenotypeCalculationArgumentCollection genotypeArgs = new GenotypeCalculationArgumentCollection();
         final StandardCallerArgumentCollection standardArgs = new StandardCallerArgumentCollection();
         return new MinimalGenotypingEngine(standardArgs, SAMPLES);
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 543ff6776e3..6c58aff3a59 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -1,4 +1,3 @@
-
 package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
 
 import com.google.common.collect.ImmutableMap;
@@ -1222,15 +1221,15 @@ public Object[][] getContaminationCorrectionTestData() {
         // GATK 4 calls on the uncontaminated bam
         // GATK 3 calls on the contaminated bam with contamination correction
         return new Object[][] {
-//                { contaminatedBam15Percent,
-//                  0.15,
-//                  contaminationFile,
-//                  traversalInterval,
-//                  b37_reference_20_21,
-//                  false, // VCF mode
-//                  expectedGATK4UncontaminatedCallsVCF,
-//                  expectedGATK3ContaminationCorrectedCallsVCF
-//                },
+                { contaminatedBam15Percent,
+                  0.15,
+                  contaminationFile,
+                  traversalInterval,
+                  b37_reference_20_21,
+                  false, // VCF mode
+                  expectedGATK4UncontaminatedCallsVCF,
+                  expectedGATK3ContaminationCorrectedCallsVCF
+                },
                 { contaminatedBam15Percent,
                   0.15,
                   contaminationFile,
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java
deleted file mode 100644
index 716c6e00780..00000000000
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
-
-import htsjdk.samtools.util.OverlapDetector;
-import org.broadinstitute.hellbender.GATKBaseTest;
-import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
-import org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine;
-import org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection;
-import org.broadinstitute.hellbender.utils.SimpleInterval;
-import org.broadinstitute.hellbender.utils.genotyper.SampleList;
-import org.jetbrains.annotations.NotNull;
-import org.testng.Assert;
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import static org.testng.Assert.*;
-
-public class MultiPloidyGenotyperCacheUnitTest extends GATKBaseTest {
-
-
-    @DataProvider
-    public static Object[][] getGenotyperParams() {
-        return new Object[][]{
-                {"1:10-30", 2},
-                {"1:70-85", 3},
-                {"1:80-93", 3},
-                {"1:89-92", 1}, //note that the explicitly set ploidy of 1 overrides the default ploidy 2 here
-                {"1:90-95", 1},
-                {"1:85-120", 5},
-                {"2:200", 2},
-                {"2:1-500", 4}
-        };
-    }
-
-    @Test(dataProvider = "getGenotyperParams")
-    public void testGettingGenotypers(String interval, int expectedPloidy){
-        final var detector = getOverlapDetector();
-        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
-        final MinimalGenotypingEngine genotypingEngine = genotypingCache.getGenotypingEngine(new SimpleInterval(interval));
-        Assert.assertEquals(genotypingEngine.getGenotypeArgs().samplePloidy, expectedPloidy);
-    }
-
-    @NotNull
-    private OverlapDetector<SimpleCount> getOverlapDetector() {
-        final var counts = List.of(
-                getCount("1:80", 3),
-                getCount("1:90-95", 1),
-                getCount("1:100-110", 5),
-                getCount("2:85-90", 4));
-        return OverlapDetector.create(counts);
-    }
-
-    @Test
-    public void testReturnsTheSameGenotyper(){
-        final var detector = getOverlapDetector();
-        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
-        final MinimalGenotypingEngine genotypingEngine = genotypingCache.getGenotypingEngine(new SimpleInterval("1:10-20"));
-        final MinimalGenotypingEngine genotypingEngine2 = genotypingCache.getGenotypingEngine(new SimpleInterval("2:10-20"));
-        Assert.assertSame(genotypingEngine, genotypingEngine2);
-    }
-
-    @Test
-    public void testGetDefaultBeforeInit() {
-        final var detector = getOverlapDetector();
-        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
-        Assert.assertNotNull(genotypingCache.getDefaultGenotypingEngine());
-    }
-
-    private MinimalGenotypingEngine getEngine(int ploidy){
-        final var args = new StandardCallerArgumentCollection();
-        args.genotypeArgs.samplePloidy = ploidy;
-        final var samples = SampleList.singletonSampleList("sample1");
-        return new MinimalGenotypingEngine(args, samples);
-    }
-
-    private static SimpleCount getCount(String location, int count){
-        return new SimpleCount(new SimpleInterval(location), count);
-    }
-
-}
\ No newline at end of file

From 0e442968519988aef5c7dc88d502b1146fdd4463 Mon Sep 17 00:00:00 2001
From: rickymagner <81349869+rickymagner@users.noreply.github.com>
Date: Fri, 8 Dec 2023 17:16:20 -0500
Subject: [PATCH 5/5] Update new test for copying arg sync

---
 .../haplotypecaller/HaplotypeCallerIntegrationTest.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 6c58aff3a59..cddb87c5dac 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -1050,7 +1050,7 @@ public void testArgCollectionCopiesAreSynchronized() {
         hcArgs.applyBQD = !hcArgs.applyBQD;
         hcArgs.dontGenotype = !hcArgs.dontGenotype;
         hcArgs.standardArgs.annotateAllSitesWithPLs = !hcArgs.standardArgs.annotateAllSitesWithPLs;
-        hcArgs.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered = !hcArgs.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered;
+        hcArgs.standardArgs.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = !hcArgs.standardArgs.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED;
 
         // Create copy with different ploidy and check tweaked values (and one control non-changed value) remain in sync
         HaplotypeCallerArgumentCollection hcArgsCopy = hcArgs.copyWithNewPloidy(3);
@@ -1058,7 +1058,7 @@ public void testArgCollectionCopiesAreSynchronized() {
         Assert.assertEquals(hcArgs.dontGenotype, hcArgsCopy.dontGenotype);
         Assert.assertEquals(hcArgs.standardArgs.annotateAllSitesWithPLs, hcArgsCopy.standardArgs.annotateAllSitesWithPLs);
         Assert.assertEquals(hcArgs.standardArgs.CONTAMINATION_FRACTION, hcArgsCopy.standardArgs.CONTAMINATION_FRACTION);
-        Assert.assertEquals(hcArgs.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered, hcArgsCopy.standardArgs.genotypeArgs.annotateNumberOfAllelesDiscovered);
+        Assert.assertEquals(hcArgs.standardArgs.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED, hcArgsCopy.standardArgs.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED);
 
         // Modify other values of copy and check they are now distinct, i.e. a "deep copy" was created above
         hcArgsCopy.applyBQD = !hcArgsCopy.applyBQD;