plink merge Error & an issue with --split-cat-pheno

[jie huang]

Dear Chris:

Please see my log file at https://github.com/jielab/001/blob/main/files/plink.log. Center is the 22 centers for UK Biobank data. Although the log file says that --split-cat-pheno: 1 categorical covariate converted to 22 covariates and the error message is elsewhere, this command runs completely fine once I remove --split-cat-pheno center. Don't know how to correctly adjust for the 22 centers in UKB.

Another issue that I recently encountered with  PLINK is merging data.

• When I run plink1 --merge-list merge_list.txt, it says Error: 1 variant with 3+ alleles present. 
• When I run plink2 --merge-list, it says --merge-list is retired.  Use --pmerge-list instead. 
• When I run plink2 --pmerge-list merge_list.txt, it says Error: Non-concatenating --pmerge[-list] is under development.

Please advise how to avoid issues like this when merging data.

Thank you & Best regards,

Jie

[Chris Chang]

From the --split-cat-pheno documentation:

* 'omit-most' causes the largest category to be omitted (breaking ties in favor of removing the first-seen category), while 'omit-last' always removes the last-seen category. (It is often necessary to omit one category to avoid creating linear dependence between the covariates, which breaks --glm.)
...

Note that --glm does not require you to preprocess categorical covariates with this command; it automatically executes "--split-cat-pheno omit-most covar-01" on them.

(I just added the last sentence today, so your memory isn't playing tricks on you if you don't remember seeing it earlier.)

As for merge, if there's only "1 variant" with 3+ alleles present, it's probably ".", and you should preprocess all the input files with e.g. --set-all-var-ids or --set-missing-var-ids before retrying.

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