From e05af54f3eaa9100bbddb2267aead8a72c3b7423 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 7 Nov 2010 03:39:57 +0000
Subject: [PATCH] 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
---
 .../gatk/walkers/genotyper/GridSearchAFEstimation.java      | 3 ++-
 .../genotyper/SNPGenotypeLikelihoodsCalculationModel.java   | 6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
index 6d4cbdc27..23f52471d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -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);
         }
     }
-}
\ No newline at end of file
+}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index cffa3c465..e744c5ca3 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -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());