From 7f721eab0bb39599fabf7d742cc5311b254b8943 Mon Sep 17 00:00:00 2001
From: epiercehoffman <epierceh@broadinstitute.org>
Date: Mon, 17 May 2021 22:28:45 -0400
Subject: [PATCH] add -w flag to grep for varID searches in 04b (#139)

---
 wdl/CombineReassess.wdl | 2 +-
 wdl/Module04b.wdl       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/wdl/CombineReassess.wdl b/wdl/CombineReassess.wdl
index 1f9a9408a..3409ce776 100644
--- 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
index c633e3986..0733cc3d9 100644
--- 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