From 9357bee921c23ecbe60d1b5602fd2bf09ab54348 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Feb 2011 17:25:50 +0000
Subject: [PATCH] Don't skip tri-allelic alleles passed in - just choose the
 first one.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5293 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/SNPGenotypeLikelihoodsCalculationModel.java | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index cc86a75ed..3372a955b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -73,14 +73,14 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
             final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
             if ( vcInput == null )
                 return null;
-            if ( !vcInput.isBiallelic() ) {
-                logger.info("Record at position " + ref.getLocus() + " is not bi-allelic; skipping...");
-                return null;
-            }
             if ( !vcInput.isSNP() ) {
                 logger.info("Record at position " + ref.getLocus() + " is not a SNP; skipping...");
                 return null;
             }
+            if ( !vcInput.isBiallelic() ) {
+                logger.info("Record at position " + ref.getLocus() + " is not bi-allelic; choosing the first allele...");
+                //return null;
+            }
             bestAlternateAllele = vcInput.getAlternateAllele(0).getBases()[0];
         } else {
             initializeBestAlternateAllele(refBase, contexts);