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Fix to Enable SelectVariants to drop sites with * allele as only ALT #5129

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merged 6 commits into from
Aug 30, 2018
Merged

Fix to Enable SelectVariants to drop sites with * allele as only ALT #5129

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8aee9d3
Attempt to fix #1525
kvinter1 Aug 21, 2018
d9fb0d5
Attempt to fix #1525
kvinter1 Aug 22, 2018
fde9671
Attempt to fix #1525
kvinter1 Aug 22, 2018
cc14c23
Attempt to fix #1525
kvinter1 Aug 22, 2018
9dd443a
Created tests for spanning deletions.
kvinter1 Aug 22, 2018
8c78964
Fixed issues found in PR review.
kvinter1 Aug 23, 2018
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8 changes: 6 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants.java
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Expand Up @@ -569,8 +569,8 @@ public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext
}
final VariantContext filteredGenotypeToNocall = setFilteredGenotypesToNocall ? builder.make(): sub;

// Not excluding non-variants or subsetted polymorphic variants AND including filtered loci or subsetted variant is not filtered
if ((!XLnonVariants || filteredGenotypeToNocall.isPolymorphicInSamples()) && (!XLfiltered || !filteredGenotypeToNocall.isFiltered())) {
// Not excluding non-variants OR (subsetted polymorphic variants AND not spanning deletion) AND (including filtered loci OR subsetted variant) is not filtered
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This is still really hard to read. Maybe give examples of things that will pass here?

if ((!XLnonVariants || (filteredGenotypeToNocall.isPolymorphicInSamples() && !checkOnlySpanDel(filteredGenotypeToNocall))) && (!XLfiltered || !filteredGenotypeToNocall.isFiltered())) {

// Write the subsetted variant if it matches all of the expressions
boolean failedJexlMatch = false;
Expand All @@ -596,6 +596,10 @@ public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext
}
}

private boolean checkOnlySpanDel(VariantContext vc){
return vc.getAlternateAlleles().size() == 1 && vc.getAlternateAllele(0).basesMatch(Allele.SPAN_DEL);
}

/**
* Get the genotype filters
*
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48 changes: 48 additions & 0 deletions ...g/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
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Expand Up @@ -343,6 +343,54 @@ public void testNoGTs() throws IOException {
spec.executeTest("testNoGTs--" + testFile, this);
}

@Test
public void testRemoveMonomorphAfterSNSelect() throws IOException {
final String testFile = getToolTestDataDir() + "spanning_deletion.vcf";
final String samplesFile = "NA1";
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Really this is a sample name rather than a samplesFile so can you change the variable name?


final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + samplesFile + " --remove-unused-alternates --exclude-non-variants", testFile),
Collections.singletonList(getToolTestDataDir() + "expected/" + "testSelectVariants_RemoveMonomorphAfterSNSelect.vcf")
);
spec.executeTest("test will make sure line is removed when only monomorphic allele exists" + testFile, this);
}

@Test
public void testRemoveSingleSpanDelAlleleNoSpanDel() throws IOException {
final String testFile = getToolTestDataDir() + "spanning_deletion.vcf";
final String samplesFile = "NA1";

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + samplesFile + " --remove-unused-alternates --exclude-non-variants", testFile),
Collections.singletonList(getToolTestDataDir() + "expected/" + "testSelectVariants_RemoveSingleSpanDelAlleleNoSpanDel.vcf")
);
spec.executeTest("test will not remove variant line where '*' is only ALT allele because none exist" + testFile, this);
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I don't see how this is different from the above test.

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Did you want to use a different input file where the * is in a heterozygous genotype?

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My mistake. They are the same. Turns out the test technically tests two things at once, I deleted the second instance.

}

@Test
public void testRemoveSingleSpanDelAlleleExNonVar() throws IOException {
final String testFile = getToolTestDataDir() + "spanning_deletion.vcf";
final String samplesFile = "NA2";

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + samplesFile + " --remove-unused-alternates", testFile),
Collections.singletonList(getToolTestDataDir() + "expected/" + "testSelectVariants_RemoveSingleSpanDelAlleleExNoVar.vcf")
);
spec.executeTest("test will not remove variant line where '*' is only ALT allele because --exclude-non-variants not called --" + testFile, this);
}

@Test
public void testRemoveSingleSpanDelAllele() throws IOException {
final String testFile = getToolTestDataDir() + "spanning_deletion.vcf";
final String samplesFile = "NA2";

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + samplesFile + " --exclude-non-variants --remove-unused-alternates", testFile),
Collections.singletonList(getToolTestDataDir() + "expected/" + "testSelectVariants_RemoveSingleSpanDelAllele.vcf")
);
spec.executeTest("test removes variant line where '*' is only ALT allele --" + testFile, this);
}

@Test
public void testSelectFromMultiAllelic() throws IOException {
final String testFile = getToolTestDataDir() + "multi-allelic.bi-allelicInGIH.vcf";
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33 changes: 33 additions & 0 deletions .../variantutils/SelectVariants/expected/testSelectVariants_RemoveMonomorphAfterSNSelect.vcf
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@@ -0,0 +1,33 @@
##fileformat=VCFv4.2
##ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
##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=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=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 NA1
20 20 . A T 4490.20 . AC=1;AF=0.500;AN=2;DP=80 GT:AD:DP:GQ:PL 0/1:1,0:80:3:0,3,32
33 changes: 33 additions & 0 deletions ...ers/variantutils/SelectVariants/expected/testSelectVariants_RemoveSingleSpanDelAllele.vcf
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##fileformat=VCFv4.2
##ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
##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=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=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 NA2
20 14 . GCCCCCACCC G 4490.20 . AC=2;AF=1.00;AN=2;DP=80 GT:AD:DP:GQ:PL 1/1:1,79,0:80:99:2233,233,0,2244,234,2333
34 changes: 34 additions & 0 deletions ...iantutils/SelectVariants/expected/testSelectVariants_RemoveSingleSpanDelAlleleExNoVar.vcf
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##fileformat=VCFv4.2
##ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
##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=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=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 NA2
20 14 . GCCCCCACCC G 4490.20 . AC=2;AF=1.00;AN=2;DP=80 GT:AD:DP:GQ:PL 1/1:1,79,0:80:99:2233,233,0,2244,234,2333
20 20 . A * 4490.20 . AC=2;AF=1.00;AN=2;DP=80 GT:AD:DP:GQ:PL 1/1:1,0:80:11:0,11,100
33 changes: 33 additions & 0 deletions ...ntutils/SelectVariants/expected/testSelectVariants_RemoveSingleSpanDelAlleleNoSpanDel.vcf
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##fileformat=VCFv4.2
##ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
##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=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=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 NA1
20 20 . A T 4490.20 . AC=1;AF=0.500;AN=2;DP=80 GT:AD:DP:GQ:PL 0/1:1,0:80:3:0,3,32
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