From 902cf84448fb52a22d25f0ea7cd52a6dddb00d49 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 Nov 2009 04:10:32 +0000
Subject: [PATCH] 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
---
 .../genotyper/JointEstimateGenotypeCalculationModel.java    | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
index aa227afd5..1d16ee6e5 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -293,9 +293,10 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
         }
 
         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
-        if ( !ALL_BASE_MODE && phredScaledConfidence < CONFIDENCE_THRESHOLD )
+        // return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero
+        if ( !ALL_BASE_MODE && (bestAFguess == 0 || phredScaledConfidence < CONFIDENCE_THRESHOLD) )
             return new Pair<List<Genotype>, GenotypeLocusData>(null, null);
 
         ArrayList<Genotype> calls = new ArrayList<Genotype>();
@@ -331,7 +332,6 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
                 ((ConfidenceBacked)locusdata).setConfidence(phredScaledConfidence);
             }
             if ( locusdata instanceof AlleleFrequencyBacked ) {
-                int bestAFguess = findMaxEntry(alleleFrequencyPosteriors[indexOfMax]).second;
                 ((AlleleFrequencyBacked)locusdata).setAlleleFrequency((double)bestAFguess / (double)(frequencyEstimationPoints-1));
                 AlleleFrequencyBacked.AlleleFrequencyRange range = computeAFrange(alleleFrequencyPosteriors[indexOfMax], frequencyEstimationPoints-1, bestAFguess, ALLELE_FREQUENCY_RANGE);
                 ((AlleleFrequencyBacked)locusdata).setAlleleFrequencyRange(range);