How to calculate r2 for IMPUTE2
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2.3 years ago
raalsuwaidi ▴ 100

Hi all,

I was finally able with all the help to remove some SNPs from the vcf file and then run it through IMPUTE2.

This means I have the original vcf and the imputed vcf, how do run r2 analysis?

Is there a specific tool or scripts where I can give it the original file and the output file for comparison and indication for quality? I am really new in this area

r2 IMPUTE2 • 386 views
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