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The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.
(Dec 06, 2023 at 16:46) anh151 said:
Hello,
I am trying to run LD score regression on my GWAS results in order to assess polygenecity vs confounding from my population. My GWAS was a linear regression of ~8.8 million variants and 900 samples.
Note
The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.
(Dec 06, 2023 at 16:46) anh151 said:
Hello,
I am trying to run LD score regression on my GWAS results in order to assess polygenecity vs confounding from my population. My GWAS was a linear regression of ~8.8 million variants and 900 samples.
I followed the example available at the link below. I was able to replicate the analysis one of the 1kg datasets available through hail on chromsome 21.
https://ibg.colorado.edu/cdrom2023/session/Day-5b%20Hail%20I,%20Tim%20Poterba/2021_IBG_Hail/05-advanced-hail-functionality.ipynb
However, when I run it on my GWAS data, I get the results shown below. Can you provide some more information on what would cause an NaN result?
Thanks,
Andrew
(Dec 12, 2023 at 16:00) anh151 said:
Couldn’t get it to work and couldn’t figure out why. Ended up using the ldsc package using the example below:
https://cloufield.github.io/GWASTutorial/08_LDSC/
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