From 3ea4e9e6d804c1b9e2342393a998f0f5d3f64d82 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 11 Mar 2021 09:22:39 +0100
Subject: [PATCH] gatk4: fix option for Haplotypecaller
---
src/nf_modules/gatk4/main.nf | 1 -
1 file changed, 1 deletion(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index add285f5..ef296cb8 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -176,7 +176,6 @@ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
-R ${fasta} \
-I ${bam} \
-ERC GVCF \
- -variant_index_type LINEAR -variant_index_parameter 128000 \
-O ${file_id}.gvcf
"""
}
--
GitLab