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VariantEval now decides whether a variant is not confidently called using BestVsNetxBest if genotypes are being evaluated and BestVsRef if not (variant discovery only). Also, the absolute value of the BestVsRef LOD (getVariantionConfidence) is used so that confident reference calls (if the GELI has output them) will show up in the final table as reference calls rather than no calls. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1347 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-07-30 21:54:06 +00:00
parent 1c648a2d5f
commit 845488ff94
1 changed files with 10 additions and 2 deletions
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12
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -155,8 +155,16 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
AllelicVariant eval = (AllelicVariant)tracker.lookup("eval", null);
//if ( eval!=null ) System.out.printf("Eval: %f %d %b%n", eval.getVariationConfidence(), minDiscoveryQ, eval.getVariationConfidence() < minDiscoveryQ);
if ( eval != null && eval.getVariationConfidence() < minDiscoveryQ )
eval = null;
if ( eval != null ) {
out.println(eval);
if ( evalContainsGenotypes ) {
// Genotyping - use best vs. next best lod
if ( eval.getConsensusConfidence() < minDiscoveryQ ) eval = null;
} else {
// Variant discovery - use best vs. reference lod
if ( Math.abs(eval.getVariationConfidence()) < minDiscoveryQ ) eval = null;
}
}
// update stats about all of the SNPs
updateAnalysisSet(ALL_SNPS, eval, tracker, ref, context);