From f978c25b9daec76bddc7e89b43c03f85aef8306b Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 4 Oct 2010 13:56:04 +0000
Subject: [PATCH] Perhaps both, Eric. Perhaps both.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4422 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/SelectVariants.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index c2dcf9553..26ec24fd6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -256,7 +256,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                 else if (g.isHomVar()) { alleleCount += 2; }
                 
                 String dp = (String) g.getAttribute("DP");
-                if (dp != null && ! dp.equals(VCFConstants.MISSING_DEPTH_v3)) {
+                if (dp != null && ! dp.equals(VCFConstants.MISSING_DEPTH_v3) && ! dp.equals(VCFConstants.MISSING_VALUE_v4) ) {
                     depth += Integer.valueOf(dp);
                 }
             }