Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 6 commits into from
Aug 30, 2018
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 11 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -569,8 +569,13 @@ 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
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is still really hard to read. Maybe give examples of things that will pass here?

// If exclude non-variants argument is not called, filtering will NOT occur.
// If exclude non-variants is called, and a spanning deletion exists, the spanning deletion will be filtered
// If exclude non-variants is called, it is a polymorphic variant, but not a spanning deletion, filtering will not occur
// True iff exclude-filtered is not called or the filteredGenotypeToNocall is not already filtered

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 +601,10 @@ 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
*
Expand Down
40 changes: 38 additions & 2 deletions ...g/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -343,13 +343,49 @@ public void testNoGTs() throws IOException {
spec.executeTest("testNoGTs--" + testFile, this);
}

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

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + sampleName + " --remove-unused-alternates --exclude-non-variants", testFile),
Collections.singletonList(getToolTestDataDir() + "expected/" + "testSelectVariants_RemoveSingleSpanDelAlleleNoSpanDel.vcf")
);
spec.executeTest("test encounter no instance of '*' as only ALT allele and ensure line is removed when only monomorphic allele exists" + testFile, this);
}

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

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + sampleName + " --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 sampleName = "NA2";

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + sampleName + " --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";
final String samplesFile = getToolTestDataDir() + "GIH.samples.args";
final String sampleName = getToolTestDataDir() + "GIH.samples.args";

final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(" -sn " + samplesFile + " --exclude-non-variants --remove-unused-alternates", testFile),
baseTestString(" -sn " + sampleName + " --exclude-non-variants --remove-unused-alternates", testFile),
Collections.singletonList(getToolTestDataDir() + "expected/" + "testSelectVariants_MultiAllelicExcludeNonVar.vcf")
);
spec.executeTest("test select from multi allelic with exclude-non-variants --" + testFile, this);
Expand Down
33 changes: 33 additions & 0 deletions ...ers/variantutils/SelectVariants/expected/testSelectVariants_RemoveSingleSpanDelAllele.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 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
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
##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
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
34 changes: 34 additions & 0 deletions ...broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/spanning_deletion.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
##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,assembly=b37>
##contig=<ID=21,length=48129895,assembly=b37>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 NA2
20 14 . GCCCCCACCC G 4490.20 . . GT:AD:DP:GQ:PL 0/0:1,0,79:80:99:2284,2287,2316,207,237,0 1/1:1,79,0:80:99:2233,233,0,2244,234,2333
20 20 . A T,* 4490.20 . . GT:AD:DP:GQ:PL 0/1:1,0,79:80:99:2284,2287,2316,207,237,0 2/2:1,79,0:80:99:2233,233,0,2244,234,2333