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Clinical-Genomics / raredisease

CG's rare disease pipeline in next flow, see the main repo here 👇
https://github.com/nf-core/raredisease
MIT License
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gnomAD MNV #4

Open dnil opened 5 years ago

dnil commented 5 years ago

These guys are really productive!

A current solution to MNV extraction:

https://github.com/macarthur-lab/gnomad_mnv

Described in:

https://www.biorxiv.org/content/biorxiv/early/2019/03/10/573378.1.full.pdf

Pretty common with stop-gain-rescue - and occasionally the reverse - so well worth investigating.

With VCF data on gnomAD available at

https://gnomad.broadinstitute.org/downloads/

henrikstranneheim commented 2 years ago

Will not add in MIP. Could be discussed in https://github.com/nf-core/raredisease when the time comes

dnil commented 1 year ago

Hi! I think the intention was to move this here and reopen, right? 😊 This is a great time to add some level of MNV recognition, at least som limited read level phasing. It has impact not only for coding regions, but also for intergenic variants, and for variant filtering and ranking, as the individual constituent variants may be somewhat common, but together as a functional "haplotype" they can be both rare and causative.