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Thank you for providing this useful resource. There were a few setup steps in the README that may be missing, and I'm noting them here in case it is useful for others:
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Install the rlist R package.
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The PheWAS repo needs to be downloaded/cloned. (It is appears that this step was supposed to be automated in the script, but it doesn't always work.)
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A
.famfile needs to be added to the "data" directory, e.g.,ukb.12345_cal_chr1_v3.fam. I created it with PLINK2. My PLINK2 call looked something like this:plink2 --sample ukb12345_c1_b0_v3_s67890.sample --bgen ukb_imp_chr1_v3.bgen --make-bed
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