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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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error in first step #132

Closed bnj50 closed 1 year ago

bnj50 commented 1 year ago

hi for the step 1 in my directory I have 1) baselineLF_v2.2.UKB.polyfun.tar.gz, 2) my sumstats (a gwas summary statistics that has header for SNPs, Chr, BP and A1 and A2). And my command are:

(polyfun-1.0.0) bash-4.2$ python /usr/local/polyfun/extract_snpvar.py --sumstats --out --allow-missing --snps SNPS usage: extract_snpvar.py [-h] --snps SNPS --out OUT [--allow-missing] [--q Q] extract_snpvar.py: error: the following arguments are required: --out

I am not sure the cause of error might be related to python version...

appreciate your response...

best

bnj50 commented 1 year ago

it was older version of polyfun that cause this error...please ignore