From e9f7cd5491da49294f65ac78e73dadafd32dfc44 Mon Sep 17 00:00:00 2001
From: naumenko-sa <evolgenomicslab@gmail.com>
Date: Thu, 13 Dec 2018 15:36:46 -0500
Subject: [PATCH] 	modified:   cre.sh 	modified:  
 vcf.platypus.getNV.gatk3.sh

---
 cre.sh                      | 1 -
 vcf.platypus.getNV.gatk3.sh | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/cre.sh b/cre.sh
index 6832898..40058dc 100755
--- a/cre.sh
+++ b/cre.sh
@@ -210,7 +210,6 @@ function f_make_report
 	bcftools view -R ${family}-ensemble.db.txt.positions $fprefix.vcf.gz | bcftools sort | vt decompose -s - | vt uniq - -o $fprefix.subset.vcf.gz
 	tabix $fprefix.subset.vcf.gz
 	f_fix_sample_names $fprefix
-	# for some reason there was vcf.platypus.getNV.gatk3.sh - memory bug
 	vcf.platypus.getNV.sh $fprefix.subset.vcf.gz $reference
     fi
 
diff --git a/vcf.platypus.getNV.gatk3.sh b/vcf.platypus.getNV.gatk3.sh
index 9d39c7c..045a4a9 100755
--- a/vcf.platypus.getNV.gatk3.sh
+++ b/vcf.platypus.getNV.gatk3.sh
@@ -6,7 +6,7 @@ bname=`basename $1 .subset.vcf.gz`
 
 if [ -e $1 ]
 then
-    gatk3 -Xmx10G -T VariantsToTable \
+    gatk3 -T VariantsToTable \
     -R $2 \
     -V $1 \
     -F CHROM -F POS -F REF -F ALT -F TC -GF NR -GF NV \