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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 ?