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Bug fix: if the most likely allele frequency is 0, don't make a variant call (even if the Qscore for AF=1/n > threshold) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2033 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-13 04:10:32 +00:00
parent 555fb975de
commit 902cf84448
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
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@ -293,9 +293,10 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
} }
double phredScaledConfidence = -10.0 * Math.log10(alleleFrequencyPosteriors[indexOfMax][0]); double phredScaledConfidence = -10.0 * Math.log10(alleleFrequencyPosteriors[indexOfMax][0]);
int bestAFguess = findMaxEntry(alleleFrequencyPosteriors[indexOfMax]).second;
// return a null call if we don't pass the confidence cutoff // return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero
if ( !ALL_BASE_MODE && phredScaledConfidence < CONFIDENCE_THRESHOLD ) if ( !ALL_BASE_MODE && (bestAFguess == 0 || phredScaledConfidence < CONFIDENCE_THRESHOLD) )
return new Pair<List<Genotype>, GenotypeLocusData>(null, null); return new Pair<List<Genotype>, GenotypeLocusData>(null, null);
ArrayList<Genotype> calls = new ArrayList<Genotype>(); ArrayList<Genotype> calls = new ArrayList<Genotype>();
@ -331,7 +332,6 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
((ConfidenceBacked)locusdata).setConfidence(phredScaledConfidence); ((ConfidenceBacked)locusdata).setConfidence(phredScaledConfidence);
} }
if ( locusdata instanceof AlleleFrequencyBacked ) { if ( locusdata instanceof AlleleFrequencyBacked ) {
int bestAFguess = findMaxEntry(alleleFrequencyPosteriors[indexOfMax]).second;
((AlleleFrequencyBacked)locusdata).setAlleleFrequency((double)bestAFguess / (double)(frequencyEstimationPoints-1)); ((AlleleFrequencyBacked)locusdata).setAlleleFrequency((double)bestAFguess / (double)(frequencyEstimationPoints-1));
AlleleFrequencyBacked.AlleleFrequencyRange range = computeAFrange(alleleFrequencyPosteriors[indexOfMax], frequencyEstimationPoints-1, bestAFguess, ALLELE_FREQUENCY_RANGE); AlleleFrequencyBacked.AlleleFrequencyRange range = computeAFrange(alleleFrequencyPosteriors[indexOfMax], frequencyEstimationPoints-1, bestAFguess, ALLELE_FREQUENCY_RANGE);
((AlleleFrequencyBacked)locusdata).setAlleleFrequencyRange(range); ((AlleleFrequencyBacked)locusdata).setAlleleFrequencyRange(range);