modified: cre.sh

modified: vcf.platypus.getNV.gatk3.sh
naumenko-sa · Dec 13, 2018 · e9f7cd5 · e9f7cd5
1 parent 1d7a064
commit e9f7cd5
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git 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
@@ -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 \