Add tr gwas #26
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Add tr gwas #26
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gymreklab
requested changes
Nov 29, 2024
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gymreklab
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gymreklab
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Thanks for submitting this PR!
I made mostly minor comments. Once those are addressed we can merge.
See in particular the comment on automatic filtering of covariates - this can be addressed in the next PR but should be high on our list to avoid accidental filtering of covariates we didn't mean to in future runs.
| data.to_csv(covar_file_path, sep="\t", index=False) | ||
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| print(f"Done converting {args.phenotype} to plink format") | ||
| return plink_pheno,data |
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don't need to return these since they are not used. can remove this line
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Thank you for all the comments! I made the changes suggested in the comments. If everything looks good I will confirm merge. |
…in the phecode cohort
…ed on GT and remap GT
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add tr-gwas script and wdl. It enables running tr gwas genome wide on AoU cloud environment