Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Closed
LeeTL1220 opened this issue Feb 16, 2018 · 2 comments

Comments

@LeeTL1220
Copy link
Contributor

commented Feb 16, 2018

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 LeeTL1220 self-assigned this Feb 16, 2018
@LeeTL1220

This comment has been minimized.

Copy link
Contributor Author

commented Feb 16, 2018

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

@LeeTL1220

This comment has been minimized.

Copy link
Contributor Author

commented Feb 16, 2018

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
1 participant
You can’t perform that action at this time.