GATK4 Mutect2 variants IDs not shown

Question

[dganiewich]

Hi everyone!

I am a beginner using GATK, so bear with me please.

I am trying to do my variant calling with GATK4 new Mutect2 (not MuTect2), using as --germline-resource the af-only-gnomad.hg38.vcf.gz from the GATK's bundle. The command is pretty much the same as seen in the tutorial: https://software.broadinstitute.org/gatk/documentation/article?id=11136, only updated to allow it to be used in a WES.

My problem is that after successfully completing the variant calling, none of the variants have ID information, although when I compared it to a MuTect2 result several did. Basically, all of them have a "." in that field.

I checked the uncompressed gnomad.hg38.vcf.gz manually and the ID info as rsXXXXXX are there.

Any ideas on why the variant calling is not collecting the ID info from the germline resource to populate the ID field? Thank you!

Daiana

[Pierre Lindenbaum]

did you set --dbsnp ? https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.4/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php#--dbsnp

rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate. dbSNP is not used in any way for the calculations themselves.

[dganiewich]

Hi Pierre! Thank you for your answer. The page you're referring to is deprecated, as it is the BETA version. The newest one unfortunately does not have the --dbsnp option... https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php

Answer 1

[dganiewich]

Just in case someone encounters the same issue, it has been answered in: https://gatkforums.broadinstitute.org/gatk/discussion/comment/57540#Comment_57540

There is no way of populating the ID field with GATK4 Mutect2 as of today (03/29/19).

Best,

Daiana