Can extract_snpvar.py accept sumstats in hg38 coordinates instead of hg19?

omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)

MIT License

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Can extract_snpvar.py accept sumstats in hg38 coordinates instead of hg19? #171

Closed qiyanghong2020 closed 1 year ago

qiyanghong2020 commented 1 year ago

I am using a GWAS file coordinated in genome coordinates (hg38), but it seems that extract_snpvar.py and snpvar_meta.chr1_7.parquet can only accept coordinates in hg19. Could you provide me with 'snpvar_meta.chr1_7.parquet' and 'snpvar_meta.chr8_22.parquet' files based on hg38?

omerwe commented 1 year ago

UKBB released all their plink and bgen files in hg19, hence all of our files also use hg19. You can use a tool likfe LiftOver to convert your coordinates to hg19. Sorry I can't help more...

qiyanghong2020 commented 1 year ago

Thanks, definitely!