diff --git a/vcf.ensemble.getCALLERS.sh b/vcf.ensemble.getCALLERS.sh index 4843e2d..01c51b1 100755 --- a/vcf.ensemble.getCALLERS.sh +++ b/vcf.ensemble.getCALLERS.sh @@ -2,7 +2,7 @@ bname=`basename $1 .vcf.gz` -gatk-launch VariantsToTable \ +gatk VariantsToTable \ -R $2 -V $1 \ -F CHROM -F POS -F REF -F ALT -F CALLERS \ -O $bname.table diff --git a/vcf.freebayes.getAO.sh b/vcf.freebayes.getAO.sh index 3bd4213..095973c 100755 --- a/vcf.freebayes.getAO.sh +++ b/vcf.freebayes.getAO.sh @@ -4,7 +4,7 @@ bname=`basename $1 .subset.vcf.gz` if [ -e $1 ] && [ -e $2 ] then - gatk-launch VariantsToTable \ + gatk VariantsToTable \ -R $2 \ -V $1 \ -F CHROM -F POS -F REF -F ALT -F DP -GF DP -GF AO \ diff --git a/vcf.gatk.get_depth.sh b/vcf.gatk.get_depth.sh index 06e9c0f..a145d0b 100755 --- a/vcf.gatk.get_depth.sh +++ b/vcf.gatk.get_depth.sh @@ -4,7 +4,7 @@ bname=`basename $1 .subset.vcf.gz` if [ -e $1 ] then - gatk-launch VariantsToTable \ + gatk VariantsToTable \ -R $2 \ -V $1 \ -F CHROM -F POS -F REF -F ALT -F DP -GF DP -GF AD -GF GT \ diff --git a/vcf.platypus.getNV.sh b/vcf.platypus.getNV.sh index 36cafc0..613110a 100755 --- a/vcf.platypus.getNV.sh +++ b/vcf.platypus.getNV.sh @@ -4,7 +4,7 @@ bname=`basename $1 .subset.vcf.gz` if [ -e $1 ] then - gatk-launch VariantsToTable \ + gatk VariantsToTable \ -R $2 \ -V $1 \ -F CHROM -F POS -F REF -F ALT -F TC -GF NR -GF NV \ diff --git a/vcf.samtools.get_depth.sh b/vcf.samtools.get_depth.sh index c975449..73a3278 100755 --- a/vcf.samtools.get_depth.sh +++ b/vcf.samtools.get_depth.sh @@ -7,7 +7,7 @@ bname=`basename $1 .vcf.gz` if [ -e $1 ] then - gatk-launch VariantsToTable \ + gatk VariantsToTable \ -T VariantsToTable \ -R $2 \ -V $1 \