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Mutect 2 B38 germline resource #4366
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?
This Issue was generated from your [forums]
@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.