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Published 20 hours ago • verified publisher icon broadinstitute

FilterGenotypes relies on unavailable tool

Open MattWellie opened this issue 10 months ago • 1 comments

see line

FilterGenotypes.wdl -> RecalibrateGq.wdl

The RecalibrateGqTask contains a usage of XGBoostMinGqVariantFilter. The only reference to that tool in the GATK suite is this un-merged PR, and it is currently unavailable in the gatk_docker image referenced in the config for this repository.

Could you please clarify if this tool will become available, or if an alternative filtering method is available?

MattWellie avatar Sep 07 '23 00:09 MattWellie