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Enable SelectVariants to drop specific annotation fields from output …
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…vcf. (broadinstitute#5254)

Enable SelectVariants to drop specific annotation fields from output vcf. (broadinstitute#5254)
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@kachulis @EdwardDixon
kachulis authored and EdwardDixon committed Nov 9, 2018
1 parent c56470f commit 0dfb312
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Showing 7 changed files with 211 additions and 6 deletions.
60 changes: 54 additions & 6 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,7 @@
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.VariantContextUtils;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFStandardHeaderLines;
import htsjdk.variant.vcf.VCFUtils;
import htsjdk.variant.vcf.*;

import java.nio.file.Path;
import org.broadinstitute.barclay.argparser.Argument;
Expand Down Expand Up @@ -401,6 +397,18 @@ public final class SelectVariants extends VariantWalker {
@Argument(fullName="set-filtered-gt-to-nocall", optional=true, doc="Set filtered genotypes to no-call")
private boolean setFilteredGenotypesToNocall = false;

/**
* Info annotation fields to be dropped (specified by key)
*/
@Argument(fullName = "drop-info-annotation", shortName = "DA", optional = true, doc = "Info annotations to drop from output vcf. Annotations to be dropped are specified by their key.")
private List<String> infoAnnotationsToDrop = new ArrayList<>();

/**
* Genotype annotation fields to be dropped (specified by key)
*/
@Argument(fullName = "drop-genotype-annotation", shortName = "DGA", optional = true, doc = "Genotype annotations to drop from output vcf. Annotations to be dropped are specified by their key.")
private List<String> genotypeAnnotationsToDrop = new ArrayList<>();

@Hidden
@Argument(fullName="allow-nonoverlapping-command-line-samples", optional=true,
doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.")
Expand Down Expand Up @@ -505,6 +513,16 @@ public void onTraversalStart() {
actualLines = headerLines;
}
}
if (!infoAnnotationsToDrop.isEmpty()) {
for (final String infoField : infoAnnotationsToDrop) {
logger.info(String.format("Will drop info annotation: %s",infoField));
}
}
if (!genotypeAnnotationsToDrop.isEmpty()) {
for (final String genotypeAnnotation : genotypeAnnotationsToDrop) {
logger.info(String.format("Will drop genotype annotation: %s",genotypeAnnotation));
}
}

vcfWriter = createVCFWriter(outFile);
vcfWriter.writeHeader(new VCFHeader(actualLines, samples));
Expand Down Expand Up @@ -593,11 +611,37 @@ public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext

if (!failedJexlMatch &&
(!selectRandomFraction || Utils.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(filteredGenotypeToNocall);
//remove annotations being dropped and write variantcontext
final VariantContext variantContextToWrite = buildVariantContextWithDroppedAnnotationsRemoved(filteredGenotypeToNocall);
vcfWriter.add(variantContextToWrite);
}
}
}

private VariantContext buildVariantContextWithDroppedAnnotationsRemoved(final VariantContext vc) {
if (infoAnnotationsToDrop.isEmpty() && genotypeAnnotationsToDrop.isEmpty()) {
return vc;
}
final VariantContextBuilder rmAnnotationsBuilder = new VariantContextBuilder(vc);
for (String infoField : infoAnnotationsToDrop) {
rmAnnotationsBuilder.rmAttribute(infoField);
}
if (!genotypeAnnotationsToDrop.isEmpty()) {
final ArrayList<Genotype> genotypesToWrite = new ArrayList<>();
for (Genotype genotype : vc.getGenotypes()) {
final GenotypeBuilder genotypeBuilder = new GenotypeBuilder(genotype).noAttributes();
final Map<String, Object> attributes = new HashMap<>(genotype.getExtendedAttributes());
for (String genotypeAnnotation : genotypeAnnotationsToDrop) {
attributes.remove(genotypeAnnotation);
}
genotypeBuilder.attributes(attributes);
genotypesToWrite.add(genotypeBuilder.make());
}
rmAnnotationsBuilder.genotypes(GenotypesContext.create(genotypesToWrite));
}
return rmAnnotationsBuilder.make();
}

private boolean checkOnlySpanDel(VariantContext vc){
return vc.getAlternateAlleles().size() == 1 && vc.getAlternateAllele(0).basesMatch(Allele.SPAN_DEL);
}
Expand Down Expand Up @@ -777,6 +821,10 @@ private Set<VCFHeaderLine> createVCFHeaderLineList(Map<String, VCFHeader> vcfHea
headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY));

//remove header lines for info field and genotype annotations being dropped
headerLines.removeIf(l->l instanceof VCFInfoHeaderLine && infoAnnotationsToDrop.contains(((VCFInfoHeaderLine)l).getID()));
headerLines.removeIf(l->l instanceof VCFFormatHeaderLine && genotypeAnnotationsToDrop.contains(((VCFFormatHeaderLine)l).getID()));

return headerLines;
}

Expand Down
23 changes: 23 additions & 0 deletions ...g/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -877,4 +877,27 @@ public void testSetFilteredGtoNocallUpdateInfo() throws IOException {

spec.executeTest("testSetFilteredGtoNocallUpdateInfo--" + testFile, this);
}

@DataProvider(name = "dropAnnotationsDataProvider")
Object[][] dropAnnotationsDataProvider() {
return new Object[][]{
{"-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894", "testSelectVariants_DropAnnotations.vcf", "standard"},
{"-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -DA NotAnAnnotation -DGA AlsoNotAnAnnotation", "testSelectVariants_DropAnnotations.vcf", "unused_annotations"},
{"-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'FisherStrand > 10.0'", "testSelectVariants_DropAnnotationsSelectFisherStrand.vcf", "select_on_dropped_annotation"},
{"-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'RMSMAPQ > 175.0'", "testSelectVariants_DropAnnotationsSelectRMSMAPQ.vcf", "select_on_kept_annotation"},
{"-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'vc.getGenotype(\"NA11894\").getExtendedAttribute(\"RD\")>6'", "testSelectVariants_DropAnnotationsSelectRD.vcf", "select_on_dropped_genotype_annotation"},
{"-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'vc.getGenotype(\"NA11894\").getGQ()==1'", "testSelectVariants_DropAnnotationsSelectGQ.vcf", "select_on_kept_genotype_annotation"}
};
}

@Test(dataProvider = "dropAnnotationsDataProvider")
public void testDropAnnotations(String args, String expectedFile, String testName) throws IOException {
final String testFile = getToolTestDataDir() + "vcfexample2.vcf";

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(args, testFile),
Collections.singletonList(getToolTestDataDir() + "expected/" + expectedFile)
);
spec.executeTest("testDropAnnotations--" + testName, this);
}
}
33 changes: 33 additions & 0 deletions ...tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_DropAnnotations.vcf
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##fileformat=VCFv4.2
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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=AFrange,Number=2,Type=String,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=AlleleBalance,Number=1,Type=Float,Description="Allele balance">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DoC,Number=1,Type=Integer,Description="Filtered Depth">
##INFO=<ID=HomopolymerRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=MAPQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=NS,Number=1,Type=Float,Description="Number of samples">
##INFO=<ID=RMSMAPQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias">
##INFO=<ID=SpanningDeletions,Number=1,Type=Integer,Description="No spanning deletions">
##reference=human_b36_both.fasta
##source=UnifiedGenotyper
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA11894
1 10020400 . C T 30.66 . AC=1;AF=0.500;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.72;DoC=193;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=177.45;SB=-0.02;SpanningDeletions=0 GT:GQ 0/1:1
1 10020408 . C A 57.15 . AC=1;AF=0.500;AFrange=0.01-0.11,95%;AN=2;AlleleBalance=0.73;DoC=179;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=174.11;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
1 10020416 . G A,T 40.12 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.10,95%;AN=2;AlleleBalance=0.73;DoC=166;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=176.69;SB=-0.01;SpanningDeletions=0 GT:GQ 1/0:1
1 10020436 . A T 64.57 . AC=1;AF=0.500;AFrange=0.01-0.12,95%;AN=2;AlleleBalance=0.73;DoC=168;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=170.66;SB=-1.53;SpanningDeletions=0 GT:GQ 0/1:2
1 10020439 . G A,T 57.80 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.13,95%;AN=2;AlleleBalance=0.73;DoC=156;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=167.02;SB=-0.33;SpanningDeletions=0 GT:GQ 1/0:2
1 10020447 . C T 68.03 . AC=1;AF=0.500;AFrange=0.01-0.14,95%;AN=2;AlleleBalance=0.72;DoC=140;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=166.27;SB=-0.62;SpanningDeletions=0 GT:GQ 0/1:2
1 10020452 . T C 32.71 . AC=1;AF=0.500;AFrange=0.01-0.12,95%;AN=2;AlleleBalance=0.70;DoC=138;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=167.20;SB=-0.03;SpanningDeletions=0 GT:GQ 1/0:1
1 10020453 . G A,T 48.53 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.12,95%;AN=2;AlleleBalance=0.70;DoC=133;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=168.40;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:2
1 10020464 . G T 74.83 . AC=1;AF=0.500;AFrange=0.01-0.13,95%;AN=2;AlleleBalance=0.74;DoC=152;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=170.06;SB=-0.04;SpanningDeletions=0 GT:GQ 0/1:3
1 10020470 . A G,T 91.66 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.13,95%;AN=2;AlleleBalance=0.70;DoC=182;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=174.37;SB=-0.25;SpanningDeletions=0 GT:GQ 0/1:2
1 10020484 . A C,T 55.89 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.76;DoC=239;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=181.59;SB=-0.03;SpanningDeletions=0 GT:GQ 0/1:2
1 10020485 . G A,T 32.66 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.08,95%;AN=2;AlleleBalance=0.75;DoC=237;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=180.16;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
1 10020492 . T A,G 44.35 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.68;DoC=284;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=184.59;SB=-0.04;SpanningDeletions=0 GT:GQ 1/0:1
1 10020615 . C T,A 162.10 . AC=0,0;AF=0.00,0.00;AFrange=0.01-0.10,95%;AN=2;AlleleBalance=0.72;DoC=285;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=195.54;SB=-67.56;SpanningDeletions=0 GT:GQ 0/0:2
26 changes: 26 additions & 0 deletions ...antutils/SelectVariants/expected/testSelectVariants_DropAnnotationsSelectFisherStrand.vcf
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##fileformat=VCFv4.2
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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=AFrange,Number=2,Type=String,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=AlleleBalance,Number=1,Type=Float,Description="Allele balance">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DoC,Number=1,Type=Integer,Description="Filtered Depth">
##INFO=<ID=HomopolymerRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=MAPQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=NS,Number=1,Type=Float,Description="Number of samples">
##INFO=<ID=RMSMAPQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias">
##INFO=<ID=SpanningDeletions,Number=1,Type=Integer,Description="No spanning deletions">
##reference=human_b36_both.fasta
##source=UnifiedGenotyper
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA11894
1 10020408 . C A 57.15 . AC=1;AF=0.500;AFrange=0.01-0.11,95%;AN=2;AlleleBalance=0.73;DoC=179;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=174.11;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
1 10020416 . G A,T 40.12 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.10,95%;AN=2;AlleleBalance=0.73;DoC=166;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=176.69;SB=-0.01;SpanningDeletions=0 GT:GQ 1/0:1
1 10020453 . G A,T 48.53 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.12,95%;AN=2;AlleleBalance=0.70;DoC=133;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=168.40;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:2
1 10020464 . G T 74.83 . AC=1;AF=0.500;AFrange=0.01-0.13,95%;AN=2;AlleleBalance=0.74;DoC=152;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=170.06;SB=-0.04;SpanningDeletions=0 GT:GQ 0/1:3
1 10020470 . A G,T 91.66 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.13,95%;AN=2;AlleleBalance=0.70;DoC=182;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=174.37;SB=-0.25;SpanningDeletions=0 GT:GQ 0/1:2
1 10020484 . A C,T 55.89 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.76;DoC=239;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=181.59;SB=-0.03;SpanningDeletions=0 GT:GQ 0/1:2
1 10020485 . G A,T 32.66 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.08,95%;AN=2;AlleleBalance=0.75;DoC=237;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=180.16;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
25 changes: 25 additions & 0 deletions ...lkers/variantutils/SelectVariants/expected/testSelectVariants_DropAnnotationsSelectGQ.vcf
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@@ -0,0 +1,25 @@
##fileformat=VCFv4.2
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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=AFrange,Number=2,Type=String,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=AlleleBalance,Number=1,Type=Float,Description="Allele balance">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DoC,Number=1,Type=Integer,Description="Filtered Depth">
##INFO=<ID=HomopolymerRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=MAPQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=NS,Number=1,Type=Float,Description="Number of samples">
##INFO=<ID=RMSMAPQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias">
##INFO=<ID=SpanningDeletions,Number=1,Type=Integer,Description="No spanning deletions">
##reference=human_b36_both.fasta
##source=UnifiedGenotyper
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA11894
1 10020400 . C T 30.66 . AC=1;AF=0.500;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.72;DoC=193;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=177.45;SB=-0.02;SpanningDeletions=0 GT:GQ 0/1:1
1 10020408 . C A 57.15 . AC=1;AF=0.500;AFrange=0.01-0.11,95%;AN=2;AlleleBalance=0.73;DoC=179;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=174.11;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
1 10020416 . G A,T 40.12 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.10,95%;AN=2;AlleleBalance=0.73;DoC=166;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=176.69;SB=-0.01;SpanningDeletions=0 GT:GQ 1/0:1
1 10020452 . T C 32.71 . AC=1;AF=0.500;AFrange=0.01-0.12,95%;AN=2;AlleleBalance=0.70;DoC=138;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=167.20;SB=-0.03;SpanningDeletions=0 GT:GQ 1/0:1
1 10020485 . G A,T 32.66 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.08,95%;AN=2;AlleleBalance=0.75;DoC=237;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=180.16;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
1 10020492 . T A,G 44.35 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.68;DoC=284;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=184.59;SB=-0.04;SpanningDeletions=0 GT:GQ 1/0:1
25 changes: 25 additions & 0 deletions ...lkers/variantutils/SelectVariants/expected/testSelectVariants_DropAnnotationsSelectRD.vcf
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##fileformat=VCFv4.2
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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=AFrange,Number=2,Type=String,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=AlleleBalance,Number=1,Type=Float,Description="Allele balance">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DoC,Number=1,Type=Integer,Description="Filtered Depth">
##INFO=<ID=HomopolymerRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=MAPQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=NS,Number=1,Type=Float,Description="Number of samples">
##INFO=<ID=RMSMAPQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias">
##INFO=<ID=SpanningDeletions,Number=1,Type=Integer,Description="No spanning deletions">
##reference=human_b36_both.fasta
##source=UnifiedGenotyper
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA11894
1 10020408 . C A 57.15 . AC=1;AF=0.500;AFrange=0.01-0.11,95%;AN=2;AlleleBalance=0.73;DoC=179;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=174.11;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
1 10020416 . G A,T 40.12 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.10,95%;AN=2;AlleleBalance=0.73;DoC=166;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=176.69;SB=-0.01;SpanningDeletions=0 GT:GQ 1/0:1
1 10020436 . A T 64.57 . AC=1;AF=0.500;AFrange=0.01-0.12,95%;AN=2;AlleleBalance=0.73;DoC=168;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=170.66;SB=-1.53;SpanningDeletions=0 GT:GQ 0/1:2
1 10020484 . A C,T 55.89 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.76;DoC=239;HomopolymerRun=0;MAPQ0=0;NS=60;RMSMAPQ=181.59;SB=-0.03;SpanningDeletions=0 GT:GQ 0/1:2
1 10020485 . G A,T 32.66 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.08,95%;AN=2;AlleleBalance=0.75;DoC=237;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=180.16;SB=-0.02;SpanningDeletions=0 GT:GQ 1/0:1
1 10020492 . T A,G 44.35 . AC=1,0;AF=0.500,0.00;AFrange=0.01-0.09,95%;AN=2;AlleleBalance=0.68;DoC=284;HomopolymerRun=1;MAPQ0=0;NS=60;RMSMAPQ=184.59;SB=-0.04;SpanningDeletions=0 GT:GQ 1/0:1
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