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M2 Oncotator WDL needs to be able to filter variants in the VCF before rendering the MAF #4422

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LeeTL1220 opened this issue Feb 16, 2018 · 2 comments
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@LeeTL1220
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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.

@LeeTL1220
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I think most cancer analysts will want this turned on by default.

@LeeTL1220
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Though making this the default would affect @brigranger and @jnktsj. Note that old behavior would be retained.

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