The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
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.