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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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BOLT-LMM estimated beta for much smaller number of SNP than polyfun, does that matter? #140

Closed WeiCSong closed 1 year ago

WeiCSong commented 1 year ago

Hi, thanks for the great tool! I try running polypred with BOLT-LMM on UKB data, and I found that BOLT-LMM only reported PRS beta for those directly genotyped SNPs (those in .bed file) and ignored imputed SNPs (those in .bgen file; I have provided --bgenFile in BOLT). Since POLYFUN estimated posterior beta for all SNP, there would be a large gap between them in --combine-beta step. Does that matter, or did I made some mistakes? Thank you very much for your help!

omerwe commented 1 year ago

Yes, the code allows for different tools using different SNP sets (in fact this is expected, since PolyFun uses all imputed SNPs whereas all other tools effectively use only a subset of these SNPs).