Closed JingjingBai2021 closed 5 months ago
Hi I am trying to convert HIBAG imputed file to hped files but I got the following errors
My codes: python HATK.py --hla2hped --platform HIBAG --out HLA/HIBAG --rhped HLA_A.out HLA_B.out HLA_C.out NA HLA_DPB1.out HLA_DQA1.out HLA_DQB1.out HLA_DRB1.out
Hibag file format: 208-2491 208-2491 A 02,03 0201,0301 0.99676294864056 0.000802437601598225 208-2493 208-2493 A 02,34 0201,3402 0.944785376570625 7.02431224034074e-05 208-2494 208-2494 A 01,01 0101,0101 0.999999999036313 0.00582439733862464 208-2512 208-2512 A 02,03 0201,0301 0.975232580914625 0.000436120137139855 208-2514 208-2514 A 03,29 0301,2902 0.996322481060058 0.000183611256811149 208-2515 208-2515 A 03,03 0301,0301 0.975259040327707 0.000320847132575409 208-2516 208-2516 A 02,02 0201,0201 0.994795743188811 0.00713543783160078
Errors: HATK.py: error: the following arguments are required: --hg, --bfile, --pheno, --pheno-name, --imgt, --imgt-dir
Hi I am trying to convert HIBAG imputed file to hped files but I got the following errors
My codes: python HATK.py
--hla2hped
--platform HIBAG
--out HLA/HIBAG
--rhped
HLA_A.out HLA_B.out HLA_C.out NA HLA_DPB1.out HLA_DQA1.out HLA_DQB1.out HLA_DRB1.out
Hibag file format: 208-2491 208-2491 A 02,03 0201,0301 0.99676294864056 0.000802437601598225 208-2493 208-2493 A 02,34 0201,3402 0.944785376570625 7.02431224034074e-05 208-2494 208-2494 A 01,01 0101,0101 0.999999999036313 0.00582439733862464 208-2512 208-2512 A 02,03 0201,0301 0.975232580914625 0.000436120137139855 208-2514 208-2514 A 03,29 0301,2902 0.996322481060058 0.000183611256811149 208-2515 208-2515 A 03,03 0301,0301 0.975259040327707 0.000320847132575409 208-2516 208-2516 A 02,02 0201,0201 0.994795743188811 0.00713543783160078
Errors: HATK.py: error: the following arguments are required: --hg, --bfile, --pheno, --pheno-name, --imgt, --imgt-dir