Mutect2 outputting samples with AD of "."

Migwell · February 2018

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.

Sheila · February 2018

@Migwell
Hi,

Are you using the GATK4 version of Mutect2? I could not tell from the log files.

Thanks,
Sheila

Migwell · February 2018

No we aren't. We're using GATK 3.6:

INFO 06:31:36,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29

Sheila · February 2018

@Migwell
Hi,

Okay, it is best to use GATK4, as I see in my test files this issue has been fixed. You can also try a later version of GATK3, but I am not sure if this issue is fixed.

-Sheila

Mutect2 outputting samples with AD of "."

Answers