From 2b848ad8595c10902bda9bc2b80b51ce39426ab9 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Fri, 17 Oct 2014 10:28:15 -0400
Subject: [PATCH] Variants that become hom-ref after regenotyping in
 GenotypeGVCFs are now getting output in -allSites mode.

---
 .../tools/walkers/variantutils/GenotypeGVCFs.java   | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
index 1e4d7223e..2fdc0f5af 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
@@ -219,11 +219,14 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         // only re-genotype polymorphic sites
         if ( result.isVariant() ) {
             VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result);
-            if ( regenotypedVC == null )
-                return null;
-
-            regenotypedVC = GATKVariantContextUtils.reverseTrimAlleles(regenotypedVC);
-            result = addGenotypingAnnotations(originalVC.getAttributes(), regenotypedVC);
+            if ( regenotypedVC == null) {
+                if (!INCLUDE_NON_VARIANTS)
+                    return null;
+            }
+            else {
+                regenotypedVC = GATKVariantContextUtils.reverseTrimAlleles(regenotypedVC);
+                result = addGenotypingAnnotations(originalVC.getAttributes(), regenotypedVC);
+            }
         }
 
         // if it turned monomorphic then we either need to ignore or fix such sites