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VariantsToTable: Include all fields when none specified #7911

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Jun 30, 2022
Merged

VariantsToTable: Include all fields when none specified #7911

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f20763f
VariantsToTable: setting default to include all fields
orlicohen Jun 17, 2022
3e9d123
Output table includes all fields in VCF header when none specified, i…
orlicohen Jun 17, 2022
dc7ff59
added default to include all fields in VCF header when no fields spec…
orlicohen Jun 22, 2022
0a6d1ef
responding to review comments
orlicohen Jun 27, 2022
8a33af3
expected output file
orlicohen Jun 27, 2022
9b956ba
responding to review comments & added integration test
orlicohen Jun 29, 2022
cb09924
responding to review
orlicohen Jun 30, 2022
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42 changes: 35 additions & 7 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java
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Expand Up @@ -2,17 +2,14 @@

import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.barclay.argparser.Advanced;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
import picard.cmdline.programgroups.VariantEvaluationProgramGroup;
import org.broadinstitute.hellbender.engine.FeatureContext;
import org.broadinstitute.hellbender.engine.ReadsContext;
Expand Down Expand Up @@ -212,9 +209,39 @@ public void onTraversalStart() {
inputHeader = getHeaderForVariants();
outputStream = createPrintStream();

if (genotypeFieldsToTake.isEmpty() && asGenotypeFieldsToTake.isEmpty()) {
samples = Collections.emptySortedSet();
} else {
// if no fields specified, default to include all fields listed in header into table
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In the tool documentation at the top of the class, document the fact that if the tool is run without specifying any fields it defaults to including all fields declared in the VCF header. Also include an example command line for that case in the "Usage Example" section.

if(fieldsToTake.isEmpty() && genotypeFieldsToTake.isEmpty() && asFieldsToTake.isEmpty() && asGenotypeFieldsToTake.isEmpty()){
logger.warn("No fields were specified. All fields will be included in output table.");
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"All fields will be included in output table" -> "All fields declared in the VCF header will be included in the output table"


// add all mandatory VCF fields (except INFO)
for(VCFHeader.HEADER_FIELDS headerField : VCFHeader.HEADER_FIELDS.values()){
if(!headerField.name().equals(VCFHeader.HEADER_FIELDS.INFO.name())) {
fieldsToTake.add(headerField.name());
}
}

// add all INFO fields present in VCF header
for (final VCFInfoHeaderLine infoLine : inputHeader.getInfoHeaderLines()) {
fieldsToTake.add(infoLine.getID());
}

// add all FORMAT fields present in VCF header
for (final VCFFormatHeaderLine formatLine : inputHeader.getFormatHeaderLines()) {
// ensure GT field listed as first FORMAT field
if(formatLine.getID().equals("GT")) {
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"GT" -> VCFConstants.GENOTYPE_KEY

genotypeFieldsToTake.add(0, formatLine.getID());
}
else {
genotypeFieldsToTake.add(formatLine.getID());
}
}
}

// if fields specified, but none are genotype fields, set samples to empty
if (genotypeFieldsToTake.isEmpty() && asGenotypeFieldsToTake.isEmpty() && (!fieldsToTake.isEmpty() || !asFieldsToTake.isEmpty())) {
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The && (!fieldsToTake.isEmpty() || !asFieldsToTake.isEmpty()) part of this condition here is unnecessary, I believe. If the genotype fields are empty, then either the user originally specified some non-genotype fields, or we hit your new code that populates the non-genotype fields with (at a minimum) the mandatory fields from the VCF.

samples = Collections.emptySortedSet();
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This line is now indented one level too deep.

}
else {
final Map<String, VCFHeader> vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());
samples = VcfUtils.getSortedSampleSet(vcfHeaders, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);

Expand All @@ -238,6 +265,7 @@ public void onTraversalStart() {
outputStream.println("RecordID\tSample\tVariable\tValue");
} else {
final List<String> fields = new ArrayList<>();

fields.addAll(fieldsToTake);
fields.addAll(asFieldsToTake);
fields.addAll(createGenotypeFields());
Expand Down
28 changes: 28 additions & 0 deletions .../broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
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Expand Up @@ -5,6 +5,7 @@
import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
import org.testng.annotations.Test;

import java.io.File;
import java.io.IOException;
import java.util.Arrays;

Expand Down Expand Up @@ -236,4 +237,31 @@ public void testMoltenOutputWithMultipleAlleles() throws IOException {
spec.setTrimWhiteSpace(false);
spec.executeTest("testMoltenOutputWithMultipleAlleles", this);
}

@Test
public void testNoFieldsSpecified() throws IOException {
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This test case should probably be renamed testNoFieldsSpecifiedNoSamples() for clarity (and rename the corresponding expected output file)

final File inputFile = new File(getToolTestDataDir(), "extraheaderlinesdeleted_dbsnp_138.snippet.vcf");
final File outputFile = createTempFile(getToolTestDataDir(), "noFieldsSpecifiedOutput.table");
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The first argument to createTempFile() is supposed to be a prefix to the file name, and the second argument should be the file extension. So, eg., in this case you want something like:

final File outputFile = createTempFile("noFieldsSpecifiedOutput", ".table");

The temp file creation code will take care of appending a unique string to the name so that it doesn't collide with other temp files.

This same comment also applies to the outputFile in testNoFieldsSpecifiedWithSamples() below.

final File expectedFile = new File(getToolTestDataDir(), "expected.noFieldsSpecified.table");

final String[] args = new String[] {"--variant", inputFile.getAbsolutePath(),
"-O", outputFile.getAbsolutePath()};
runCommandLine(args);
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These tests don't actually assert anything. Typically (even for "this shouldn't crash" type tests) we would want to assert that the files match the expected outputs. It looks like you are most of the way there though. You already have checked in some output files that look reasonable, now all you need to do is check that the output of THIS run matches those. One way to do that is with IntegrationTestSpec.assertEqualTextFiles(). So have the tool output to a tmp file and then assert that temp file matches the new ones you checked in.


IntegrationTestSpec.assertEqualTextFiles(outputFile, expectedFile);
}

@Test
public void testNoFieldsSpecifiedWithSamples() throws IOException {
final File inputFile = new File(getToolTestDataDir(), "1000G.phase3.snippet.vcf");
final File outputFile = createTempFile(getToolTestDataDir(), "noFieldsSpecifiedWithSamplesOutput.table");
final File expectedFile = new File(getToolTestDataDir(), "expected.noFieldsSpecifiedWithSamples.table");

final String[] args = new String[] {"--variant", inputFile.getAbsolutePath(),
"-O", outputFile.getAbsolutePath()};
runCommandLine(args);

IntegrationTestSpec.assertEqualTextFiles(outputFile, expectedFile);
}

}
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After reviewing the changes to the tool, I think you should add a third integration test with a VCF that contains declarations for FORMAT fields in its header, but no samples. This will exercise the following case:

            if (samples.isEmpty()) {
                genotypeFieldsToTake.clear();
                asGenotypeFieldsToTake.clear();

It's a bit weird, but theoretically possible. You should be able to create this by making a copy of your dbsnp_138.snippet.vcf file and manually adding in a declaration for a FORMAT field to its header. Note that you can use git add to explicitly add new files to a commit.

48 changes: 48 additions & 0 deletions ...dinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/1000G.phase3.snippet.vcf
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##fileformat=VCFv4.2
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This file (1000G.phase3.snippet.vcf) is now unused. You can remove it from your branch using the git rm command.

##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1.0597 <= x < 0.1687">
##FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -5.8589 <= x < -1.0597">
##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -6.5565 <= x < -5.8589">
##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -70.77">
##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -70.77 <= x < -6.5565">
##FILTER=<ID=VQSRTrancheSNP99.90to99.95,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -96.2455 <= x < -14.2763">
##FILTER=<ID=VQSRTrancheSNP99.95to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -437.9355">
##FILTER=<ID=VQSRTrancheSNP99.95to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -437.9355 <= x < -96.2455">
##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">
##GATKCommandLine=<ID=ApplyRecalibration,Version=2.6-20-g0728857,Date="Mon Jul 01 11:58:36 EDT 2013",Epoch=1372694316825,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[20] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.lowpass.hc.recal.vcf)] recal_file=(RodBinding name=recal_file source=/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.lowpass.hc.recal.recal) tranches_file=/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.lowpass.hc.recal.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 ignore_filter=null mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/1000G.phase3.snippet.vcf --sample-name HG00096 --sample-name HG00097 --sample-name HG00099 --variant src/test/resources/large/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf --intervals 20:10000054-10000117 --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --genomicsdb-max-alternate-alleles 50 --call-genotypes false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.2.6.1-22-gd4f083d-SNAPSHOT",Date="June 21, 2022 1:46:50 PM EDT">
##GATKVersion=2.5-191-g02f8427
##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.bam.list] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/humgen/1kg/processing/production_wgs_final/chr20/.queue/scatterGather/call.for.1000G-1-sg/temp_0001_of_1000/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=200 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub graphOutput=null bamOutput=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null bamWriterType=CALLED_HAPLOTYPES dbsnp=(RodBinding name= source=UNBOUND) comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null useDebruijnAssembler=false minKmerForDebruijnAssembler=11 onlyUseKmerSizeForDebruijnAssembler=-1 kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false numPruningSamples=3 maxPathsPerSample=8 dontRecoverDanglingTails=false minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false useFilteredReadsForAnnotations=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=25 mergeVariantsViaLD=false pair_hmm_implementation=LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debug=false debugGraphTransformations=false useLowQualityBasesForAssembly=false dontTrimActiveRegions=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
##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=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##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=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
##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=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##source=SelectVariants
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099
20 10000054 . CTTTG C 504.42 PASS AC=0;AF=0.00;AN=6;BaseQRankSum=-0.975;ClippingRankSum=-2.925;DP=22;FS=1.899;InbreedingCoeff=0.0592;MQ=59.27;MQ0=0;MQRankSum=-3.212;QD=2.43;ReadPosRankSum=-0.264;VQSLOD=5.10;culprit=FS GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,119 0/0:10,0:10:29:0,29,592 0/0:10,0:10:30:0,30,598
20 10000107 . T C 263.95 PASS AC=0;AF=0.00;AN=6;BaseQRankSum=-0.444;ClippingRankSum=-3.132;DP=25;FS=0.948;InbreedingCoeff=-0.0102;MQ=59.19;MQ0=0;MQRankSum=2.292;POSITIVE_TRAIN_SITE;QD=10.56;ReadPosRankSum=0.055;VQSLOD=7.76;culprit=FS GT:AD:DP:GQ:PL 0/0:5,0:5:15:0,15,387 0/0:13,0:13:42:0,42,786 0/0:7,0:7:24:0,24,548
20 10000117 . C T 329458.17 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=10.505;ClippingRankSum=-20.658;DP=28;FS=8.305;InbreedingCoeff=0.1727;MQ=59.17;MQ0=0;MQRankSum=2.689;POSITIVE_TRAIN_SITE;QD=25.46;ReadPosRankSum=-4.688;VQSLOD=3.19;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/0:5,0:5:15:0,15,189 0/1:8,8:16:99:254,0,231 0/0:7,0:7:21:0,21,271
4 changes: 4 additions & 0 deletions ...te/hellbender/tools/walkers/variantutils/VariantsToTable/expected.noFieldsSpecified.table
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CHROM POS ID REF ALT QUAL FILTER AC CAF CLNDSDB COMMON DP DSS HD KGPROD KGPhase1 LSD REF RS RSPOS SAO SSR VC VP WGT dbSNPBuildID
20 10000092 rs183046704 T G -10.0 PASS NA [0.9991,0.0009183] NA 0 NA NA NA true true NA T 183046704 10000092 0 0 SNV 0x050000000001000014000100 1 135
20 10000107 rs188245245 T C -10.0 PASS NA [0.9982,0.001837] NA 0 NA NA NA true true NA T 188245245 10000107 0 0 SNV 0x050000000001000014000100 1 135
20 10000117 rs4816203 C T -10.0 PASS NA [0.3682,0.6318] NA 1 NA NA NA true true NA C 4816203 10000117 0 0 SNV 0x05010000000117011e000100 1 111