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atgu / ukbb_pan_ancestry

Analyses conducting GWAS across the UKBB diverse superpopulations
MIT License
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l2.M_5_50 files per chromosome #73

Open dianacornejo opened 2 years ago

dianacornejo commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

@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