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getian107 / PRScsx

Cross-population polygenic prediction
MIT License
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SUM_STATS file cannot be CSVs based on parse_sumstats function #52

Closed chen70335 closed 1 month ago

chen70335 commented 1 month ago

Hi, in your description here: "SUM_STATS_FILE (required): Full path and the file name of the GWAS summary statistics. Multiple GWAS summary statistics files are allowed and should be separated by comma." you mentioned that it should be separated by comma, but the parse_sumstats function in parse_genet.py only splits by white space/ tab on line 73.

getian107 commented 1 month ago

The description refers to the command line that specifies the directory and name of the summary statistics files. For instance:

--sst_file=Sumstats1.txt,Sumstats2.txt

Note that the two file names are separated by comma.

parse_genet.py parses the content of the summary statistics files, in which the columns (SNP, A1, A2, etc) should be separated by space or tab.