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In variant quality score recalibrator Preserve the definition of known and novel to be presence in dbSNP or not even when training with 1KG project calls. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4151 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-08-27 19:07:59 +00:00
parent 7a5f297083
commit 54355b1864
2 changed files with 3 additions and 9 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -181,22 +181,19 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
variantDatum.annotations = annotationValues;
variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0;
variantDatum.isKnown = false;
variantDatum.weight = WEIGHT_NOVELS;
variantDatum.qual = vc.getPhredScaledQual();
final DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
variantDatum.isKnown = (dbsnp!=null);
variantDatum.weight = WEIGHT_NOVELS;
if( vcHapMap != null ) {
variantDatum.isKnown = true;
variantDatum.weight = WEIGHT_HAPMAP;
} else if( vc1KG != null ) {
variantDatum.isKnown = true;
variantDatum.weight = WEIGHT_1KG;
} else if( dbsnp != null ) {
variantDatum.isKnown = true;
variantDatum.weight = WEIGHT_DBSNP;
}

5
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -214,16 +214,13 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
variantDatum.isKnown = false;
variantDatum.isKnown = (dbsnp!=null);
double knownPrior_qScore = PRIOR_NOVELS;
if( vcHapMap != null ) {
variantDatum.isKnown = true;
knownPrior_qScore = PRIOR_HAPMAP;
} else if( vc1KG != null ) {
variantDatum.isKnown = true;
knownPrior_qScore = PRIOR_1KG;
} else if( dbsnp != null ) {
variantDatum.isKnown = true;
knownPrior_qScore = PRIOR_DBSNP;
}
final double knownPrior = QualityUtils.qualToProb(knownPrior_qScore);