Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Mutect2 dont list Variant
Iam running mutect2 on capture data, with tumor normal. The data flows the "classic" way on a local wdl-pipeline with bwa =>merge=>markDup=>recal=>mutect2 (3.6).
I see the variant clearly in IGV in both tumor and normal sample and even in the bamout i created for it (see screenshot). But it dont get listed in the output vcf.
I know that mutect2 apply some hard filters to the variant, but I should see the variant in the output marked with an alt_allele_in_normal ?