Steps to running the GWAS on ANL’s servers.

  1. Install Hail and its dependencies
  2. Filter genotype files
  3. Phenotype and Covariate Files
  4. Set up GWAS environment

Install Hail

This was done by Tom Brettin. Hail is working on the nucleus machine, but not washington at the moment.

Filter Genotype Files

Downstream analysis can be a lot faster with a smaller genetic dataset. We filtered for individuals in the brain imaging cohort, and for typical GWAS population conditions: white British ancestry, not related to others in cohort, good SNP call rate, etc.

The exact list of eids is at /vol/bmd/meliao/data/eids/intersection_brain_asthma.txt, which is so named because the sample filters wre taken from the ukbREST example asthma query. The filtering was run with plink using file

This filtering has mostly been done in plink2.

Phenotype and Covariate Files

Set up GWAS environment

There is a hail environment available on the ANL servers accessible by the command

conda activate /vol/bmd/software/condaenvs/hail

Interpret Results


Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

Suggest changes

If you find any mistakes (including typos) or want to suggest changes, please feel free to edit the source file of this page on Github and create a pull request.