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 \