From 35b90d22958d55f49e14d0ae161a12d517a6fc81 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 26 Nov 2010 03:54:26 +0000 Subject: [PATCH] Don't compute SB for ref calls git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4735 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 9c1dd99bb..44ffa4f29 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -228,7 +228,7 @@ public class UnifiedGenotyperEngine { attributes.put(VCFConstants.DOWNSAMPLED_KEY, true); - if ( !UAC.NO_SLOD ) { + if ( !UAC.NO_SLOD && bestAFguess != 0 ) { final boolean DEBUG_SLOD = false; // the overall lod