Cleaning/prepping GWAS statistics

martinjzhang / scDRS

Single-cell disease relevance score (scDRS)

https://martinjzhang.github.io/scDRS/

MIT License

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Closed rbutleriii closed 2 years ago

rbutleriii commented 2 years ago

Hello, I couldn't find it in the paper. For these GWAS traits, do you do any pruning prior to magma? (i.e. exclude HLA region, limit to Hapmap3 SNPs)

Thanks

martinjzhang commented 2 years ago

Hi,

Sorry for the confusion! We have removed the MHC region (CHR6 25-34MB) and restricted the summary statistics to the HAPMAP3 SNPs.

Best, Martin

rbutleriii commented 2 years ago

Thanks!