bulik/ldsc

How to obtain the file "w_hm3.snplist.bz2"

Opened this issue · 6 comments

keypanqi commented

Hi~
Can I get the file "w_hm3.snplist.bz2" from the website(https://alkesgroup.broadinstitute.org/LDSCORE/) ?
I couldn't find it on this website. Maybe, somebody can send me one. Or there is another website?
Here is my email: 1053095150@qq.com！
Thanks a lot！！！

DavisCammann commented

The SNP list (And European LD Scores) that were available originally on the LDSC wiki can be found here:
https://ibg.colorado.edu/cdrom2021/Day06-nivard/GenomicSEM_practical/eur_w_ld_chr/

There are also 3 official locations where the most up-to-date LDSC materials are stored
https://console.cloud.google.com/storage/browser/broad-alkesgroup-public-requester-pays (Need to pay for large downloads)
https://doi.org/10.5281/zenodo.7768714
https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/baselineLF_v2.2.UKB.tar.gz

  • 👍4
carolinamf commented

Hi,

even using the above mentioned websites I could not find the file: eur_w_ld_chr.tar.bz2

I don't know if possible share this file with me.

Thank for your attention.

jfores commented

Hi Carolina! The first link provided by DavisCannaman is the uncompressed folder you are looking for. eur_w_ld_chr.tar.bz2 is not a file but a folder containing multiple files including the information of the LD scores for each SNP by chromosome. In addition, you will also find the w_hm3.snplist file which is also necessary to run the genetic correlation analyses if I remember correctly!

Cheers!

J

carolinamf commented
carolinamf commented