Update NMD rule - Githubissues

bbglab / boostdm-pipeline

Learning pipeline to identify somatic SNVs under positive selection.

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Open koszulordie opened 2 months ago

koszulordie commented 2 months ago

Annotate NMD-triggering/skipping nonsense variants through the VEP plugin: http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#nmd

koszulordie commented 4 days ago

This will imply two steps:

Change the way we run VEP in the Intogen pipeline step that prepares the datasets for boostDM.
Modify the scripts in boostDM accordingly.