GWASToolKit
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swvanderlaan
A collection of scripts to run GWAS, regional, gene-oriented, or per-variant analyses.
As my data includes the X chromosome I needed to comment out line 3 below and remove the # from line 2. echo "Analysing the phenotype ${PHENOTYPE}." # for CHR...
There are different gene lists that could be used. Here's a nice overview: https://github.com/macarthur-lab/gene_lists. We should check whether we can use these.
In some cases, when for some reason a job has not returned (proper) results (e.g. an empty .error file and a properly formatted .out file), the wrap up script still...
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A collection of scripts to run GWAS, regional, gene-oriented, or per-variant analyses.