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choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis
MIT License
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plink argument for pruning wrong #9

Open jhagenberg opened 4 years ago

jhagenberg commented 4 years ago

Hi Sam,

thanks for the tutorial! I think there is an error in the description for the arguments in the following code:

plink \
    --bfile EUR \
    --keep EUR.QC.fam \
    --extract EUR.QC.snplist \
    --indep-pairwise 200 50 0.25 \
    --out EUR.QC

As far as I understand it, in plink 1.9 the first argument of --indep-pairwise is only in kb if the kb modifier is set (see the documentation), otherwise it's variant count, so in your example a window size of 200 variants.

Best regards, Jonas

choishingwan commented 4 years ago

Thanks, I have now fixed that.

Sam