Mutect2 outputting samples with AD of "."
I've setup a workflow that runs Mutect2, which completes successfully, but the AD of all variants is output as "."
This is an issue as we use the AD for downstream stages. Is there any reason this might be happening?
I have attached both the VCF that is missing the AD field, and the log from our workflow that includes the GATK logging. Everything there seems fine, but perhaps I'm missing something.