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lifebit-ai / gwas

GWAS pipeline using SAIGE
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Split gwas_filtering, step_2 SAIGE by autosomes, sex chromosomes (will only use X not Y) #54

Open cgpu opened 4 years ago

cgpu commented 4 years ago

https://github.com/lifebit-ai/gel-gwas/blob/c11b16784a9f554ba07701263c8db208b59951f3/main.nf#L160

Requirement for HWE filtering step: Subset pheno to only females, and pass this to plink --hwe step https://github.com/lifebit-ai/gel-gwas/blob/c11b16784a9f554ba07701263c8db208b59951f3/main.nf#L211

https://github.com/lifebit-ai/gel-gwas/blob/c11b16784a9f554ba07701263c8db208b59951f3/main.nf#L160-L228