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Found the cause of 80% of our non-called FNs: an excess of filtered bases were causing us to choose the wrong alternate allele. More details to dev team. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4634 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-07 03:39:57 +00:00
parent 2a8c97a4a7
commit e05af54f3e
2 changed files with 6 additions and 3 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
View File

@ -228,6 +228,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
/*
System.out.println(frequency);
for (int i = 0; i < N; i++) {
System.out.print(samples.get(i));
for (int j=0; j < 3; j++) {
System.out.print(String.valueOf(matrix[i][j]));
System.out.print(indexes[i] == j ? "* " : " ");
@ -280,4 +281,4 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
samplesToGenotypesPerAF.put(frequency, samplesToGenotypes);
}
}
}
}

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broad.tribble.util.variantcontext.Allele;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.*;
@ -115,8 +116,9 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
// calculate the sum of quality scores for each base
ReadBackedPileup pileup = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
for ( PileupElement p : pileup ) {
// ignore deletions
if ( p.isDeletion() )
// ignore deletions and filtered bases
if ( p.isDeletion() ||
(p.getRead() instanceof GATKSAMRecord && !((GATKSAMRecord)p.getRead()).isGoodBase(p.getOffset())) )
continue;
int index = BaseUtils.simpleBaseToBaseIndex(p.getBase());