From 2b7fe058c09023d5a2f78b3826a8ba09ecfde07e Mon Sep 17 00:00:00 2001
From: William Harvey <wharvey@uw.edu>
Date: Fri, 17 Nov 2023 11:24:07 -0800
Subject: [PATCH] mosaic

---
 workflow/rules/somatic_variants.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/somatic_variants.smk b/workflow/rules/somatic_variants.smk
index 3cc2a09..0f29083 100644
--- a/workflow/rules/somatic_variants.smk
+++ b/workflow/rules/somatic_variants.smk
@@ -84,7 +84,7 @@ rule sniffles_somatic:
     threads: 1
     shell:
         """
-        sniffles --somatic -i {input.merged_bam} --reference {input.ref} --output-rnames -v {output.vcf}
+        sniffles --mosaic -i {input.merged_bam} --reference {input.ref} --output-rnames -v {output.vcf}
         """