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Bringing VQSR up to date with the 1000G v2b changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6000 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-06-14 20:23:43 +00:00
parent 04ecbf10ab
commit d7430c23f8
3 changed files with 7 additions and 6 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -47,10 +47,9 @@ public class FisherStrand implements InfoFieldAnnotation, StandardAnnotation {
private static final double MIN_PVALUE = 1E-320; private static final double MIN_PVALUE = 1E-320;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( ! vc.isVariant() || vc.isFiltered() ) if ( ! vc.isVariant() || vc.isFiltered() )
return null; return null;
int[][] table; int[][] table;
if (vc.isBiallelic() && vc.isSNP()) if (vc.isBiallelic() && vc.isSNP())

5
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -101,7 +101,6 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
} }
else else
return null; return null;
} }
} }
} }
@ -168,13 +167,13 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
// Now retrieve the N most popular haplotypes // Now retrieve the N most popular haplotypes
if (consensusHaplotypeQueue.size() > 0) { if (consensusHaplotypeQueue.size() > 0) {
// Since the consensus haplotypes are in a quality-ordered priority queue, the two best haplotypes are just the first two in the queue // The consensus haplotypes are in a quality-ordered priority queue, so the best haplotypes are just the ones at the front of the queue
final Haplotype haplotype1 = consensusHaplotypeQueue.poll(); final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
List<Haplotype>hlist = new ArrayList<Haplotype>(); List<Haplotype>hlist = new ArrayList<Haplotype>();
hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60)); hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60));
for (int k=1;k < haplotypesToCompute; k++) { for (int k=1; k < haplotypesToCompute; k++) {
Haplotype haplotype2 = consensusHaplotypeQueue.poll(); Haplotype haplotype2 = consensusHaplotypeQueue.poll();
if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found
hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20)); hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20));

5
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
View File

@ -211,14 +211,17 @@ public class VariantDataManager {
try { try {
if( annotationKey.equalsIgnoreCase("QUAL") ) { if( annotationKey.equalsIgnoreCase("QUAL") ) {
value = vc.getPhredScaledQual(); value = vc.getPhredScaledQual();
} else if( annotationKey.equalsIgnoreCase("DP") ) {
value = Double.parseDouble( (String)vc.getAttribute( "DP" ) ) / Double.parseDouble( (String)vc.getAttribute( "AN" ) );
} else { } else {
value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) ); value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
if( Double.isInfinite(value) ) { value = Double.NaN; } if( Double.isInfinite(value) ) { value = Double.NaN; }
if( annotationKey.equalsIgnoreCase("InbreedingCoeff") && value > 0.01 ) { value = Double.NaN; } if( annotationKey.equalsIgnoreCase("InbreedingCoeff") && value > 0.05 ) { value = Double.NaN; }
if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble(); value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
} }
if( annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); } if( annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
if( annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
} }
} catch( final Exception e ) { } catch( final Exception e ) {