added gnomAD and ExAC scripts, and an example for filtering on allele frequency

quinlan-lab / pathoscore

pathoscore evaluates variant pathogenicity tools and scores.

MIT License

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Closed jimhavrilla closed 6 years ago

jimhavrilla commented 6 years ago

@brentp can you review this PR and merge it please when you have a moment?

brentp commented 6 years ago

I prefer to keep the README concise. can you remove the vcfanno config from the readme and just link to af.conf?

I think a 1 sentence blurb above the pathoscore.py annotate command would be sufficient.

brentp commented 6 years ago

I would:

remove the conf from readme
make this a new section under truth sets
introduce it with a sentence like: "we know that some supposed pathogenics are not because they appear as common variants in allele-freq databases..." ... you can see how to use this in af.conf (link). And we provide an example of how the gnomAD and ExAC databases could be pre-processes here: (link).

jimhavrilla commented 6 years ago

changes have been pushed. also fixed some typos/formatting in the readme

brentp commented 6 years ago

thanks. can you put af.conf in the same directory as the exac script and update the link?

jimhavrilla commented 6 years ago

done.