From 7db583f5223b1d61af7960fc4de2e37ddb56c056 Mon Sep 17 00:00:00 2001
From: rori <6863459+RoriCremer@users.noreply.github.com>
Date: Fri, 17 Sep 2021 13:39:01 -0400
Subject: [PATCH] remove normalization

---
 scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl
index cfe6a3e7ef1..5ae58f8c25b 100644
--- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl
+++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl
@@ -209,7 +209,7 @@ task ExtractAnAcAfFromVCF {
 
         echo $(date +%s)
 
-        bcftools norm -m- ~{local_input_vcf} > normalized_input.vcf
+        bcftools norm -m- -N ~{local_input_vcf} > normalized_input.vcf
 
         echo $(date +%s)
         du