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plink --bfile Workshop_samples_05-17-23_nocont_homo_common --allow-no-sex --linear --pheno phenotype.txt --pheno-name phenotype_interested_measure --out res_phenotype_interested_measure

NOTE: do the command described previously for all phenotype variables you have interest in your data. The type of test used (e.g. linear model, logistic, etc) will depend on the type of data you have.

6. Functional analysis

The effect of mutations-caused amino acid changes on protein function was predicted by a combination of tools that use sequence homology, evolutionary conservation, and protein structural information.

./mutserve annotate --input variantsfile.txt --annotation rCRS_annotation_2020-08-20.txt --output AnnotatedVariants.txt

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