add -w flag to grep for varID searches in 04b (#139)

broadinstitute · May 18, 2021 · 7f721ea · 7f721ea
1 parent 2166cd2
commit 7f721ea
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/wdl/CombineReassess.wdl b/wdl/CombineReassess.wdl
@@ -64,7 +64,7 @@ task Vcf2Bed {
     svtk vcf2bed ~{vcf} ~{vcf}.bed
     awk '{if($6!="")print $0}' ~{vcf}.bed >~{vcf}.nonempty.bed
     cut -f 4 ~{regeno_file} >regeno_variants.txt
-    fgrep -f regeno_variants.txt ~{vcf}.nonempty.bed> nonempty.txt
+    fgrep -wf regeno_variants.txt ~{vcf}.nonempty.bed> nonempty.txt
   >>>
   output {
     File nonempty="nonempty.txt"

diff --git a/wdl/Module04b.wdl b/wdl/Module04b.wdl
@@ -741,9 +741,9 @@ task ConcatRegenotypedVcfs {
   command <<<
     set -euo pipefail
     zcat ~{regeno_vcf} |fgrep "#" > head.txt
-    zcat ~{regeno_vcf} |fgrep -f ~{regeno_variants} >body.txt
+    zcat ~{regeno_vcf} |fgrep -wf ~{regeno_variants} >body.txt
     cat head.txt body.txt|bgzip -c > regeno.vcf.gz
-    zcat ~{depth_vcf} |fgrep -f ~{regeno_variants} -v |bgzip -c > no_variant.vcf.gz
+    zcat ~{depth_vcf} |fgrep -wf ~{regeno_variants} -v |bgzip -c > no_variant.vcf.gz
     vcf-concat regeno.vcf.gz no_variant.vcf.gz \
       | vcf-sort -c \
       | bgzip -c > ~{batch}.depth.regeno_final.vcf.gz