From 2a5349d8861dbeefae9de5145cc0a3a150ea19a2 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 20 Nov 2009 03:26:09 +0000
Subject: [PATCH] VariantAnnotator now adds dbsnp id if a dbsnp rod is supplied
 and it's not already set for a record

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2100 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/annotator/VariantAnnotator.java      | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 0e7f7b81d..a54089775 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -215,6 +215,12 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         VCFRecord rec = getVCFRecord(tracker, ref, context, variant);
         if ( rec != null ) {
             rec.addInfoFields(annotations);
+            // also, annotate dbsnp id if available and not already there
+            if ( rec.getID() == null || rec.getID().equals(".") ) {
+                rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null));
+                if ( dbsnp != null )
+                    rec.setID(dbsnp.getRS_ID());
+            }
             vcfWriter.addRecord(rec);
         }
     }