l2.M_5_50 files per chromosome

[dianacornejo]

Hi, I was wondering if there's any way to obtain the l2.M5_50 files by chromosome, or if you could provide the MAF column on which you based these analysis so I can do it myself!
I do not see that column in the UKBB.*.l2.ldscore.gz files
Thanks in advance

Diana

[mkanai]

Hi Diana,

Do you need per-chromosome files for LDSC's --w-ld-chr option or for other purposes? if the former, you can just use --w-ld option instead.

If the latter, MAF is not currently exported. It exists in the Hail Table located here gs://ukb-diverse-pops-public/ld_release/UKBB.{POP}.ldscore.ht. Please refer to these lines about how we generated .M_5_50 files from .ht.

Best,
Masa

[dianacornejo]

@mkanai thanks for your reply! Is there a way I can download the hail table in .txt format for the EUR population? I do not understand how to access the resource in aws. Thanks a lot