From 4bc632aaa8d0cdf3775ed48f25da57c3180cbcfe Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 2 Apr 2012 10:09:00 -0400
Subject: [PATCH] Fix for --multiallelic in Unified Genotyper.

---
 tools/gatk/unified_genotyper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 41ea01555dc..de046faaccd 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -138,6 +138,7 @@
                 --excludeAnnotation "${annotation}"
             #end for
         #end if
+        ${analysis_param_type.multiallelic}
         '
 ##        #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
 ##            -p '--annotation "SnpEff"'
@@ -145,7 +146,6 @@
 ##        #else:
 ##            -p '--excludeAnnotation "SnpEff"'
 ##        #end if
-        ${analysis_param_type.multiallelic}
     #end if
   </command>
   <inputs>