From 2acfd5aaffacc30ca2e3fcb66ce2a663911ad3f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Mon, 1 Jul 2019 14:18:12 +0200
Subject: [PATCH] add panel of normals option to mutect2

---
 gatk.wdl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gatk.wdl b/gatk.wdl
index e76a93e..50a26f0 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -258,6 +258,7 @@ task MuTect2 {
         String outputVcf
         String tumorSample
         String? normalSample
+        File? panelOfNormals
         Array[File]+ intervals
 
         Int memory = 4
@@ -274,6 +275,7 @@ task MuTect2 {
         -I ~{sep=" -I " inputBams} \
         -tumor ~{tumorSample} \
         ~{"-normal " + normalSample} \
+        ~{"--panel-of-normals " + panelOfNormals} \
         -O ~{outputVcf} \
         -L ~{sep=" -L " intervals}
     }
-- 
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