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} """