RajLabMSSM / echoLD

echoverse module: LD downloading and processing
0 stars 0 forks source link

Liftover `dat` before querying LD panel #5

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

@omerwe could you remind me which genome build the pre-computed UKB LD panel is in? I'm sure I asked this a long time ago but I can't seem to recall now.

https://data.broadinstitute.org/alkesgroup/UKBB_LD

omerwe commented 2 years ago

@bschilder I'm afraid it's hg19... (this is the ref panel with which UKB was originally imputed, so there's nothing much I can do about it 🤷 )

bschilder commented 2 years ago

Thanks for the quick reply @omerwe! No problem at all, my strategy is actually to lift over the data I'm using to query the LD panel (rather than try and liftover the LD panel itself).

I've added this to the echoLD documentation so I don't forget.

Hope all is well with you 😄

Best, Brian

bschilder commented 2 years ago

Updated documentation for ?echoLD::get_LD. Screenshot 2022-08-28 at 12 02 01