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After merging with Yossi's fix I can confirm that the AD is fixed when going through the HC too. Added similar fixes to DP and FS annotations too.

This commit is contained in:
Eric Banks 2012-10-05 16:37:42 -04:00
parent b7639d7ceb
commit e8a6460a33
4 changed files with 23 additions and 17 deletions
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8
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -83,16 +83,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
//
// testing AD for reduced reads
// testing reduced reads
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void HCtestADAnnotationInReducedBam() {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("6ac31dbea0ffc289b6feadb47457d427")); //TODO: once the HC is fixed, update MD5
executeTest("HC test AD Annotation when calling on a ReducedRead BAM", spec);
Arrays.asList("864abe729828248333aee14818c1d2e1"));
executeTest("HC calling on a ReducedRead BAM", spec);
}

9
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
View File

@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -49,8 +50,12 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
if ( perReadAlleleLikelihoodMap.size() == 0 )
return null;
for ( Map.Entry<String, PerReadAlleleLikelihoodMap> sample : perReadAlleleLikelihoodMap.entrySet() )
depth += sample.getValue().getNumberOfStoredElements();
for (PerReadAlleleLikelihoodMap maps : perReadAlleleLikelihoodMap.values() ) {
for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
final GATKSAMRecord read = el.getKey();
depth += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1);
}
}
}
else
return null;

16
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -71,7 +72,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
}
else if (stratifiedPerReadAlleleLikelihoodMap != null) {
// either SNP with no alignment context, or indels: per-read likelihood map needed
final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount());
final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc);
return pValueForBestTable(table, null);
}
else
@ -235,14 +236,13 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
* allele2 # #
* @return a 2x2 contingency table
*/
private static int[][] getContingencyTable( final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
final Allele ref, final Allele alt) {
private static int[][] getContingencyTable( final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap, final VariantContext vc) {
final Allele ref = vc.getReference();
final Allele alt = vc.getAltAlleleWithHighestAlleleCount();
int[][] table = new int[2][2];
for (PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
if ( el.getKey().isReducedRead() ) // ignore reduced reads
continue;
final boolean matchesRef = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(ref,true);
final boolean matchesAlt = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(alt,true);
@ -254,7 +254,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
int row = matchesRef ? 0 : 1;
int column = isFW ? 0 : 1;
table[row][column]++;
final GATKSAMRecord read = el.getKey();
table[row][column] += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1);
}
}
@ -275,7 +276,6 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (PileupElement p : sample.getValue().getBasePileup()) {
// if ( ! RankSumTest.isUsableBase(p, false) || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
if ( ! RankSumTest.isUsableBase(p, false) ) // ignore deletions
continue;
@ -291,7 +291,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
int row = matchesRef ? 0 : 1;
int column = isFW ? 0 : 1;
table[row][column]+=p.getRepresentativeCount();
table[row][column] += p.getRepresentativeCount();
}
}
}

7
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -438,18 +438,19 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
executeTest("test calling on reads with Ns in CIGAR", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing AD for reduced reads
// testing reduced reads
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testADAnnotationInReducedBam() {
public void testReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("84486c88a0fd1ae996a6402490db8492"));
executeTest("test AD Annotation when calling on a ReducedRead BAM", spec);
executeTest("test calling on a ReducedRead BAM", spec);
}
}