FilterGenotypes relies on unavailable tool

[MattWellie]

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?

[epiercehoffman]

The downstream filtering steps are still in development. Further documentation is forthcoming once they are finalized. However, they can still be used in the meantime.

The docker used for RecalibrateGq, gq_recalibrator_docker, is defined in the dockers.json as us.gcr.io/broad-dsde-methods/markw/gatk:mw-tb-form-sv-filter-training-data-899360a. You can see which docker is used by looking at the input JSON template provided for FilterGenotypes.wdl here.