I would like to do a WES analysis of rare variants in UKB using RAP.
I have experience with GWAS in the past using Plink in a Linux environment.
I am having trouble understanding how to use Plink and other tools in the Linux environment.
As a beginner, could you give me any advice?
I have the CLI on my Windows PC.
You should search the forum for prior posts on the topic. or check the dnanexus gitbook. (linked below)
I have a github with code for running both rare variant as well as gwas using dx run cli. If you have the linux tools or cigwyn installed on your windows computer you can use these scripts.
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You should search the forum for prior posts on the topic. or check the dnanexus gitbook. (linked below)
I have a github with code for running both rare variant as well as gwas using dx run cli. If you have the linux tools or cigwyn installed on your windows computer you can use these scripts.
GWAS:
https://community.dnanexus.com/s/question/0D5t00000416OTeCAM/performing-gwas-on-rap-using-dx-toolkit-and-swissarmyknife
Rare Variant Analysis with rvtests
https://community.dnanexus.com/s/question/0D5t0000048rxnoCAA/rare-variant-analysis-scripts-using-swissarmyknife-and-rvtests
You can also use regenie for rare varaint analysis, but I never wrote up how to do that with swissarmy knife.
https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/using-regenie-to-generate-variant-masks
-Phil
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