Konrad Karczewski

Sorry, I'm not sure I'm following. The examples you have are all SNPs, so I don't see how this affects indels. For the SNPs, yes, grabbing the ref context and...

Oh! I just realized this was two different suggestions (separated by "Additionally") - sorry about that! Yes, this seems sensible, though it could be worthwhile to have a documented example...

they won't be, but as this is a pretty big breaking change, lets make sure all pipelines that use this package are fixed before we do remove them

I'd like to second this request. Is there a plan to implement Provisioned IOPS in Starcluster?

I would probably advocate for these two ideas to be independent. We can get this into gnomad_methods, test it out, make sure people can use it, and then when we...

I'm not quite sure what the question is, but yes, if you don't really have many trios or sib pairs, the transmitted and sibling singleton stuff won't do much. It...

Yep, looks like a Gencode v19 annotation issue that's been resolved in future releases (GRCh38, but for that matter Gencode 24liftover37). I think we should keep it as is for...

I need an example of this to proceed. If anyone has one, would be happy to fix.

Ah, makes sense. I feel like I've seen them with gene symbol, but maybe that's mostly colloquial (and made a bit difficult due to versioning).

Hmm, how are you invoking loftee? Also, is this GRCh37 or 38?