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Many users do not want mutations filtered in the VCF to show up in the MAF file.
Two things:
Update the default M2 WDL to use broadinstitute/oncotator:1.9.7.0 docker image.
Add an optional flag to prune filtered mutations to the Oncotator task. If this is set to True, add the following to the oncotator command: --collapse-filter-cols --prune-filter-cols
This is unnecessary for the CNV WDL.
The text was updated successfully, but these errors were encountered:
Many users do not want mutations filtered in the VCF to show up in the MAF file.
Two things:
Update the default M2 WDL to use
broadinstitute/oncotator:1.9.7.0
docker image.Add an optional flag to prune filtered mutations to the Oncotator task. If this is set to True, add the following to the oncotator command:
--collapse-filter-cols --prune-filter-cols
This is unnecessary for the CNV WDL.
The text was updated successfully, but these errors were encountered: