Enable SelectVariants to drop specific annotation fields from output vcf.

src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants.java

@@ -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;
@@ -404,6 +400,18 @@ 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.")
@@ -508,6 +516,16 @@ 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));
@@ -596,11 +614,37 @@ 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);
     }
@@ -780,6 +824,10 @@ 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;
     }
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -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);
+    }
 }

src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_DropAnnotations.vcf

@@ -0,0 +1,33 @@
+##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	

src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_DropAnnotationsSelectFisherStrand.vcf

@@ -0,0 +1,26 @@
+##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	

src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_DropAnnotationsSelectGQ.vcf

@@ -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	

src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_DropAnnotationsSelectRD.vcf

@@ -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	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