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change --num-pc to 10
aryarm
approved these changes
Oct 23, 2024
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Looks great! My only comment is that perhaps it might be helpful to have the other inputs (ancestry file, covar file) as command line argument in case you ever want to specify them via the command line? But no worries, if not Update: oops I just realized that you're already doing that. Nevermind me |
aryarm
reviewed
Oct 23, 2024
| parser.add_argument("--GQ", help="Apply minimun genotype score QC", type=int, default=20) | ||
| args = parser.parse_args() | ||
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add script to convert phenotype_covar.csv to plink friendly version