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1. Discoverable base calculations don't care about Genotypes (use Variation's PError regardless of whether the call is ref or var - it's the correct value even for ref calls). 

2. Call a base genotypable if any of the Genotypes is above the threshold (you can't assume there's a single Genotype associated with the Variation).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2306 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-10 04:26:06 +00:00
parent a45adadf1f
commit 0fae798b3a
1 changed files with 9 additions and 6 deletions
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15
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java
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@ -68,15 +68,18 @@ public class CallableBasesAnalysis extends BasicVariantAnalysis implements Genot
// For every threshold, updated discoverable and callable // For every threshold, updated discoverable and callable
for (int i = 0; i < thresholds.length; i++) { for (int i = 0; i < thresholds.length; i++) {
double threshold = thresholds[i]; double threshold = thresholds[i];
Genotype genotype = ((VariantBackedByGenotype)eval).getCalledGenotype();
// update discoverable // update discoverable
if ( eval.isSNP() && eval.getNegLog10PError() >= threshold) if ( eval.getNegLog10PError() >= threshold )
discoverable_bases[i]++; discoverable_bases[i]++;
if ( eval.isReference() && genotype.getNegLog10PError() >= threshold)
discoverable_bases[i]++; List<Genotype> genotypes = ((VariantBackedByGenotype)eval).getGenotypes();
if ( genotype.getNegLog10PError() >= threshold) for ( Genotype g : genotypes ) {
genotypable_bases[i]++; if ( g.getNegLog10PError() >= threshold ) {
genotypable_bases[i]++;
break;
}
}
} }
return null; return null;