add microbial mode

broadinstitute · Oct 1, 2020 · 7dc51cd · 7dc51cd
1 parent 1f81c82
commit 7dc51cd
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Showing 3 changed files with 20 additions and 3 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
@@ -44,6 +44,7 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection
     public static final String NORMAL_LOG_10_ODDS_LONG_NAME = "normal-lod";
     public static final String IGNORE_ITR_ARTIFACTS_LONG_NAME = "ignore-itr-artifacts";
     public static final String MITOCHONDRIA_MODE_LONG_NAME = "mitochondria-mode";
+    public static final String MICROBIAL_MODE_LONG_NAME = "microbial-mode";
     public static final String CALLABLE_DEPTH_LONG_NAME = "callable-depth";
     public static final String PCR_SNV_QUAL_LONG_NAME = "pcr-snv-qual";
     public static final String PCR_INDEL_QUAL_LONG_NAME = "pcr-indel-qual";

diff --git a/...broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java b/...broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java
@@ -43,6 +43,13 @@ public class M2FiltersArgumentCollection {
     @Argument(fullName = M2ArgumentCollection.MITOCHONDRIA_MODE_LONG_NAME, optional = true, doc = "Set filters to mitochondrial defaults")
     public boolean mitochondria = false;
 
+    /**
+     * Mitochondria mode excludes the filters {@link ClusteredEventsFilter}, {@link MultiallelicFilter},
+     * {@link FilteredHaplotypeFilter}, {@link FragmentLengthFilter}, and {@link GermlineFilter}
+     */
+    @Argument(fullName = M2ArgumentCollection.MICROBIAL_MODE_LONG_NAME, optional = true, doc = "Set filters to microbial defaults")
+    public boolean microbial = false;
+
 
     /**
      * Hard filter thresholds
@@ -62,12 +69,13 @@ public class M2FiltersArgumentCollection {
     private static final int DEFAULT_MAX_ALT_ALLELES = 1;
     private static final int DEFAULT_MIN_UNIQUE_ALT_READS = 0;
     private static final int DEFAULT_MIN_MEDIAN_MAPPING_QUALITY = 30;
+    private static final int DEFAULT_MIN_MEDIAN_MAPPING_QUALITY_FOR_MICROBIAL = 20;
     private static final int DEFAULT_MIN_MEDIAN_BASE_QUALITY = 20;
     private static final int DEFAULT_MAX_MEDIAN_FRAGMENT_LENGTH_DIFFERENCE = 10000;
     private static final int DEFAULT_MIN_MEDIAN_READ_POSITION = 1;
     private static final double DEFAULT_MAX_N_RATIO = Double.POSITIVE_INFINITY;
     private static final int DEFAULT_MIN_READS_ON_EACH_STRAND = 0;
-    private static final double DEFAULT_MAX_NUMT_FRACTION = 0.85;
+//    private static final double DEFAULT_MAX_NUMT_FRACTION = 0.85;
     private static final double DEFAULT_MIN_AF = 0;
 
     @Argument(fullName = MAX_EVENTS_IN_REGION_LONG_NAME, optional = true, doc = "Maximum events in a single assembly region.  Filter all variants if exceeded.")
@@ -81,6 +89,9 @@ public class M2FiltersArgumentCollection {
 
     @Argument(fullName = MIN_MEDIAN_MAPPING_QUALITY_LONG_NAME, optional = true, doc="Minimum median mapping quality of alt reads")
     public int minMedianMappingQuality = DEFAULT_MIN_MEDIAN_MAPPING_QUALITY;
+    public int getMinMedianMappingQuality() {
+        return microbial && minMedianMappingQuality == DEFAULT_MIN_MEDIAN_MAPPING_QUALITY ? DEFAULT_MIN_MEDIAN_MAPPING_QUALITY_FOR_MICROBIAL : minMedianMappingQuality;
+    }
 
     @Argument(fullName = MIN_MEDIAN_BASE_QUALITY_LONG_NAME, optional = true, doc="Minimum median base quality of alt reads")
     public int minMedianBaseQuality = DEFAULT_MIN_MEDIAN_BASE_QUALITY;

diff --git a/.../org/broadinstitute/hellbender/tools/walkers/mutect/filtering/Mutect2FilteringEngine.java b/.../org/broadinstitute/hellbender/tools/walkers/mutect/filtering/Mutect2FilteringEngine.java
@@ -284,7 +284,7 @@ public void writeFilteringStats(final Path filteringStats) {
     private void buildFiltersList(final M2FiltersArgumentCollection MTFAC) {
         filters.add(new TumorEvidenceFilter());
         filters.add(new BaseQualityFilter(MTFAC.minMedianBaseQuality));
-        filters.add(new MappingQualityFilter(MTFAC.minMedianMappingQuality, MTFAC.longIndelLength));
+        filters.add(new MappingQualityFilter(MTFAC.getMinMedianMappingQuality(), MTFAC.longIndelLength));
         filters.add(new DuplicatedAltReadFilter(MTFAC.uniqueAltReadCount));
         filters.add(new StrandArtifactFilter());
         filters.add(new ContaminationFilter(MTFAC.contaminationTables, MTFAC.contaminationEstimate));
@@ -311,13 +311,18 @@ private void buildFiltersList(final M2FiltersArgumentCollection MTFAC) {
             filters.add(new ReadOrientationFilter(artifactTables));
         }
 
-        if (!MTFAC.mitochondria) {
+        if (!MTFAC.mitochondria && !MTFAC.microbial) {
             filters.add(new ClusteredEventsFilter(MTFAC.maxEventsInRegion));
             filters.add(new MultiallelicFilter(MTFAC.numAltAllelesThreshold));
             filters.add(new FragmentLengthFilter(MTFAC.maxMedianFragmentLengthDifference));
             filters.add(new PolymeraseSlippageFilter(MTFAC.minSlippageLength, MTFAC.slippageRate));
             filters.add(new FilteredHaplotypeFilter(MTFAC.maxDistanceToFilteredCallOnSameHaplotype));
             filters.add(new GermlineFilter(MTFAC.tumorSegmentationTables));
         }
+
+        if (MTFAC.microbial) {
+            filters.add(new PolymeraseSlippageFilter(MTFAC.minSlippageLength, MTFAC.slippageRate));
+        }
+
     }
 }