search

brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
249 stars 23 forks source link

use RankSum's for filtering #36

Closed brentp closed 4 years ago

brentp commented 5 years ago

via @adw222 many variants that pass other filters often have high MQRankSum scores, this could be a filter or added to default list of tsv exports.

genomics-geek commented 5 years ago

I noticed these fields are not accessible in INFO. I assumed all fields in INFO would be.

brentp commented 5 years ago

they are available, I am using them in some cases. can you expand on what you're seeing?

genomics-geek commented 5 years ago

I take that back, yes it is working. For some reason before I was getting unknown attribute but could be related to what I was working on with this https://github.com/brentp/slivar/issues/27#issuecomment-534774933.

brentp commented 5 years ago

i also have a pending change in dev that prevents it from stopping (just issues a warning) if, for example if you ask for BaseQRankSum but it happens to be missing from a few variants. I'll get the release out this week or next.

genomics-geek commented 5 years ago

It was probably related to that. Thanks!

brentp commented 4 years ago

closing for now. Please re-open with more info if problem persists.