gatk-launch > gatk to be compatible with bcbio 1.1.0

naumenko-sa · Sep 10, 2018 · 3e226ac · 3e226ac
1 parent d005ab1
commit 3e226ac
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -7,7 +7,7 @@ bname=`basename $1 .vcf.gz`
 
 if [ -e $1 ]
 then
-    gatk-launch VariantsToTable \
+    gatk VariantsToTable \
      -T VariantsToTable \
      -R $2 \
      -V $1 \