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Bug fix for general ploidy model: when choosing the most likely alternate allele(s), you need to weight the likelihood mass by the ploidy of the specific alleles (otherwise all alt alleles will have the same probability). This fixes Yossi's issue with pooled validation calling. This may brek integration tests, but I will leave that to GdA to handle.

This commit is contained in:
Eric Banks 2012-10-19 12:01:45 -04:00
parent 27d8d3f51e
commit d3cf37dfaf
1 changed files with 2 additions and 1 deletions
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3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
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@ -128,6 +128,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
* @return list of numAllelesToChoose most likely alleles
*/
private static final int PL_INDEX_OF_HOM_REF = 0;
private static List<Allele> chooseMostLikelyAlternateAlleles(VariantContext vc, int numAllelesToChoose, int ploidy) {
final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
final LikelihoodSum[] likelihoodSums = new LikelihoodSum[numOriginalAltAlleles];
@ -143,7 +144,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
// by convention, first count coming from getAlleleCountFromPLIndex comes from reference allele
for (int k=1; k < acCount.length;k++) {
if (acCount[k] > 0)
likelihoodSums[k-1].sum += likelihoods[PLindexOfBestGL];
likelihoodSums[k-1].sum += acCount[k] * (likelihoods[PLindexOfBestGL] - likelihoods[PL_INDEX_OF_HOM_REF]);
}
}