search

hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts
Apache License 2.0
20 stars 4 forks source link

Update isovar usage #19

Open tavinathanson opened 8 years ago

tavinathanson commented 8 years ago

@iskandr is changing a few things around. Also, his comment from before:

My only suggestion would be to maybe increase the minimum MAPQ to 1 and if you're ultimately using the counts of neoepitopes with >= 3 spanning reads then this will be very sensitive to the degree of exonic coverage. Maybe normalize by number of reads mapping to exons?

tavinathanson commented 8 years ago

Also see https://github.com/hammerlab/bladder-analyses/issues/4#issuecomment-222227666 (sorry to link to a private repo).