From 613d69e26fae5120b9d005dab298a5c2b3e9091a Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Wed, 30 Oct 2024 16:46:49 -0400
Subject: [PATCH] Removing --contamination-table from FilterMutectCalls due to
 causing low recall with SEQC2 TN pair

---
 workflow/rules/somatic.smk | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/somatic.smk b/workflow/rules/somatic.smk
index 02c69b2..eda5f93 100644
--- a/workflow/rules/somatic.smk
+++ b/workflow/rules/somatic.smk
@@ -609,12 +609,14 @@ rule gatk_filter_mutect2:
         config['tools']['gatk4'],
         config['tools']['vcftools'],
     shell: """
-    # Mutect2 orien bias filter
+    # Mutect2 orien bias filter,
+    # removing the contamination filter 
+    # option due to causing low recall
+    # with SEQC2 truth set
     gatk FilterMutectCalls \\
         -R {params.genome} \\
         -V {input.vcf} \\
         --ob-priors {input.orien} \\
-        --contamination-table {input.summary} \\
         -O {output.vcf} \\
         --stats {input.stats} 
     """