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pjgreer / ukb-rap-tools

Scripts and workflows for use analyzing UK Biobank data from the DNANexus Research Analysis Platform
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WGS GWAS #18

Open frahimov opened 5 months ago

frahimov commented 5 months ago

Hello, I would like to thank you for such an incredible and well-documented resource, which is way better than the DNAnexus'es own pipelines/instructions. I was wondering if you have figured how to run GWAS using the WGS data, specifically using with the DRAGEN pVCF files for input. Thank you

pjgreer commented 5 months ago

Alas, I have not had time to work on it. I have also been having some issues with the UKB RAP, but once those are worked out I hope to look into it. One of the major issues I foresee will be having to reduce the number of subjects to make the analysis tractable. This will require more upfront work in identifying proper matched case-control populations. The datasets will end up being HUGE for rare variant analysis (thus the need to have a smaller cohort), but we might be able to get away with most of the data when filtering by MAF > 0.001 and missingness.

Check back in the coming weeks, I might get something together by then.

-Phil