From 94b41eb45c1a7662b39f4e2a64ef5b19f7531d4f Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Wed, 10 Jan 2024 10:55:36 +0800
Subject: [PATCH] bug

---
 wdl/call_mutation.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wdl/call_mutation.wdl b/wdl/call_mutation.wdl
index c5c65d2..9645af8 100755
--- a/wdl/call_mutation.wdl
+++ b/wdl/call_mutation.wdl
@@ -267,7 +267,7 @@ task mutation_calling_tissue_control {
         vcf_add_tag_msi.pl ${output_dir}/mutation/${name}.raw.snp_indel.vcf ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf ${probe} t
 
         vcf_filter.py -i ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf \
-        -o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf
+        -o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf \
         -e 'INFO/STATUS="StrongSomatic" | ( INFO/STATUS="LikelySomatic" && FORMAT/AF[0] > 3*FORMAT/AF[1] )'
 
         vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \