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

Mutect 2 B38 germline resource #4366

Closed
sooheelee opened this Issue Feb 7, 2018 · 2 comments

Comments

Projects
None yet
3 participants
@sooheelee
Contributor

sooheelee commented Feb 7, 2018

Quick forum question for @davidbenjamin @takutosato. How to set --af-of-alleles-not-in-resource for WGS data when coverage in gnomAD resource is combination of WES and WGS?


Thanks a lot @shlee for the information. Can you point me towards where the README is? I suspected the liftover might be more involved than it appears (it explains why one isn't already floating around) and it would be good to understand how you've done it. Can I ask why you don't recommend cross-map?

Looking at your tutorial you suggest altering --af-of-alleles-not-in-resource for exome data. What would you recommend for whole genomes - which would include non-coding regions only covered by the 16k and coding regions covered by the ~200,000?

Thanks again

Dan

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/comment/45767#Comment_45767

@davidbenjamin

This comment has been minimized.

Show comment
Hide comment
@davidbenjamin

davidbenjamin Feb 7, 2018

Contributor

@sooheelee That's a pitfall we haven't solved yet. I think we'll eventually infer the value locally from the AC of nearby variants in the germline resource. Until then, I would use the smaller value i.e. the one for coding regions. The only possible harm would be a very few rare germline events that aren't in gnomAD, whereas if you set it too high you risk filtering true somatic events.

Contributor

davidbenjamin commented Feb 7, 2018

@sooheelee That's a pitfall we haven't solved yet. I think we'll eventually infer the value locally from the AC of nearby variants in the germline resource. Until then, I would use the smaller value i.e. the one for coding regions. The only possible harm would be a very few rare germline events that aren't in gnomAD, whereas if you set it too high you risk filtering true somatic events.

@sooheelee

This comment has been minimized.

Show comment
Hide comment
@sooheelee

sooheelee Feb 9, 2018

Contributor

I've passed the word along. Thank you.

Contributor

sooheelee commented Feb 9, 2018

I've passed the word along. Thank you.

@sooheelee sooheelee closed this Feb 9, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment