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A couple of fixes for writing VCFs in GenotypeConcordance #810

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Jun 1, 2017
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A couple of fixes for writing VCFs in GenotypeConcordance #810

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23 changes: 12 additions & 11 deletions src/main/java/picard/vcf/GenotypeConcordance.java
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Expand Up @@ -416,6 +416,11 @@ private void writeVcfTuple(final VcfTuple tuple, final VariantContextWriter writ
callContext = tuple.rightVariantContext.get();
}

//Don't write symbolic alleles to output VCF
if (truthContext != null && truthContext.isSymbolic() || callContext != null && callContext.isSymbolic()) {
return;
}

// Get the alleles for each genotype. No alleles will be extracted for a genotype if the genotype is
// mixed, filtered, or missing.
final Alleles alleles = normalizeAlleles(truthContext, TRUTH_SAMPLE, callContext, CALL_SAMPLE);
Expand All @@ -432,14 +437,10 @@ private void writeVcfTuple(final VcfTuple tuple, final VariantContextWriter writ
final List<Allele> truthAlleles = alleles.truthAlleles();
final List<Allele> callAlleles = alleles.callAlleles();

// Get the alleles present at this site for both samples to use for the output variant context.
// Get the alleles present at this site for both samples to use for the output variant context, but remove no calls.
final Set<Allele> siteAlleles = new HashSet<>();
if (truthContext != null) {
siteAlleles.addAll(truthContext.getAlleles());
}
if (callContext != null) {
siteAlleles.addAll(callContext.getAlleles());
}
siteAlleles.addAll(allAlleles);
siteAlleles.remove(Allele.NO_CALL);
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please add a symbolic allele to your test.

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It seems that GenotypeConcordance doesn't support symbolic alleles:

Note that only SNP and INDEL variants are considered, MNP, Symbolic, and Mixed classes of variants are not included.

That said, a symbolic allele does cause it to blow up if you are writing an output VCF. In this case what should the tool do? Skip that site or blow up with an appropriate error message?


// Initialize the variant context builder
final VariantContext initialContext = (callContext == null) ? truthContext : callContext;
Expand Down Expand Up @@ -739,17 +740,17 @@ final protected static Alleles normalizeAlleles(final VariantContext truthContex
// Truth reference is shorter than call reference
final String suffix = getStringSuffix(callRef, truthRef, "Ref alleles mismatch between: " + truthContext + " and " + callContext);
final int insertIdx = truthRef.length();
truthAllele1 = spliceOrAppendString(truthAllele1, suffix, insertIdx);
truthAllele2 = spliceOrAppendString(truthAllele2, suffix, insertIdx);
truthAllele1 = truthAllele1.equals(Allele.NO_CALL_STRING) ? truthAllele1 : spliceOrAppendString(truthAllele1, suffix, insertIdx);
truthAllele2 = truthAllele2.equals(Allele.NO_CALL_STRING) ? truthAllele2 : spliceOrAppendString(truthAllele2, suffix, insertIdx);
truthRef = truthRef + suffix;

}
else if (truthRef.length() > callRef.length()) {
// call reference is shorter than truth:
final String suffix = getStringSuffix(truthRef, callRef, "Ref alleles mismatch between: " + truthContext + " and " + callContext);
final int insertIdx = callRef.length();
callAllele1 = spliceOrAppendString(callAllele1, suffix, insertIdx);
callAllele2 = spliceOrAppendString(callAllele2, suffix, insertIdx);
callAllele1 = callAllele1.equals(Allele.NO_CALL_STRING) ? callAllele1 : spliceOrAppendString(callAllele1, suffix, insertIdx);
callAllele2 = callAllele2.equals(Allele.NO_CALL_STRING) ? callAllele2 : spliceOrAppendString(callAllele2, suffix, insertIdx);
callRef = callRef + suffix;
}
else {
Expand Down
35 changes: 35 additions & 0 deletions src/test/java/picard/vcf/GenotypeConcordanceTest.java
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Expand Up @@ -25,6 +25,7 @@
package picard.vcf;

import htsjdk.samtools.metrics.MetricsFile;
import htsjdk.samtools.metrics.StringHeader;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.IOUtil;
import htsjdk.variant.variantcontext.Allele;
Expand Down Expand Up @@ -100,6 +101,8 @@ public class GenotypeConcordanceTest {

private static final String NORMALIZE_ALLELES_TRUTH = "normalize_alleles_truth.vcf";
private static final String NORMALIZE_ALLELES_CALL = "normalize_alleles_call.vcf";
private static final String NORMALIZE_NO_CALLS_TRUTH = "normalize_no_calls_truth.vcf";
private static final String NORMALIZE_NO_CALLS_CALL = "normalize_no_calls_call.vcf";

@AfterClass
public void tearDown() {
Expand Down Expand Up @@ -572,4 +575,36 @@ public void testNoCallVariants() {

Assert.assertEquals(genotypeConcordance.instanceMain(new String[0]), 0);
}

@Test
public void testNormalizeAllelesForWritingVCF() throws FileNotFoundException {
final File truthVcfPath = new File(TEST_DATA_PATH.getAbsolutePath(), NORMALIZE_NO_CALLS_TRUTH);
final File callVcfPath = new File(TEST_DATA_PATH.getAbsolutePath(), NORMALIZE_NO_CALLS_CALL);
final File outputBaseFileName = new File(OUTPUT_DATA_PATH, "MultipleRefAlleles");
final File outputContingencyMetrics = new File(outputBaseFileName.getAbsolutePath() + GenotypeConcordance.CONTINGENCY_METRICS_FILE_EXTENSION);
outputContingencyMetrics.deleteOnExit();

final GenotypeConcordance genotypeConcordance = new GenotypeConcordance();
genotypeConcordance.TRUTH_VCF = truthVcfPath;
genotypeConcordance.TRUTH_SAMPLE = "truth";
genotypeConcordance.CALL_VCF = callVcfPath;
genotypeConcordance.CALL_SAMPLE = "truth";
genotypeConcordance.OUTPUT = new File(OUTPUT_DATA_PATH, "MultipleRefAlleles");
genotypeConcordance.OUTPUT_VCF = true;

Assert.assertEquals(genotypeConcordance.instanceMain(new String[0]), 0);
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can you also read in the metrics file and validate the results in it, rather than just checking that the program didn't blowup?

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done


final MetricsFile<GenotypeConcordanceContingencyMetrics, Comparable<?>> output = new MetricsFile<GenotypeConcordanceContingencyMetrics, Comparable<?>>();
output.read(new FileReader(outputContingencyMetrics));

for (final GenotypeConcordanceContingencyMetrics metrics : output.getMetrics()) {
if(metrics.VARIANT_TYPE == VariantContext.Type.INDEL){
Assert.assertEquals(metrics.TP_COUNT, 3);
Assert.assertEquals(metrics.TN_COUNT, 3);
Assert.assertEquals(metrics.FP_COUNT, 0);
Assert.assertEquals(metrics.FN_COUNT, 0);
Assert.assertEquals(metrics.EMPTY_COUNT, 2);
}
}
}
}
43 changes: 43 additions & 0 deletions testdata/picard/vcf/normalize_no_calls_call.vcf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
##fileformat=VCFv4.1
##FILTER=<ID=Uncertain,Description="Uncertain genotype due to reason in filter INFO field">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Net Genotype quality across all datasets, defined as difference between most likely and next most likely genotype likelihoods">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Net Genotype across all datasets">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##fileDate=20130719
##phasing=none
##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
##source=SelectVariants
##variants_justified=left
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT truth
1 1 . TCAAGGG TGGG 22132 PASS set=Intersection GT:GQ 0/1:99
1 10 . TCAACAA TCAA 22132 PASS set=Intersection GT:GQ 0/1:99
1 100 . TCAACAA TCAACAAGG 10461 PASS set=Intersection GT:GQ 0/1:99
1 1000 . TCAACAA T 10461 PASS set=Intersection GT:GQ ./.
1 1100 . TCAACAA T 10461 PASS set=Intersection GT:GQ 0/1:99
1 1200 . TCAACAA T 10461 PASS set=Intersection GT:GQ ./.
1 1300 . TCAACAA <ID> 10461 PASS set=Intersection GT:GQ 0/1:99
42 changes: 42 additions & 0 deletions testdata/picard/vcf/normalize_no_calls_truth.vcf
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@@ -0,0 +1,42 @@
##fileformat=VCFv4.1
##FILTER=<ID=Uncertain,Description="Uncertain genotype due to reason in filter INFO field">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Net Genotype quality across all datasets, defined as difference between most likely and next most likely genotype likelihoods">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##fileDate=20130719
##phasing=none
##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
##source=SelectVariants
##variants_justified=left
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT truth
1 1 . TCAA T 22132 PASS set=Intersection GT:GQ 0/1:99
1 10 . TCAA T 22132 PASS set=Intersection GT:GQ 0/1:99
1 100 . TCAA TCAAGG 10461 PASS set=Intersection GT:GQ 0/1:99
1 1000 . TCAA T 10461 PASS set=Intersection GT:GQ ./.
1 1100 . TCAA T 10461 PASS set=Intersection GT:GQ ./.
1 1200 . TCAA T 10461 PASS set=Intersection GT:GQ 0/1:99
1 1300 . TCAA <ID> 10461 PASS set=Intersection GT:GQ 0/1:99