How to calculate r2 for IMPUTE2
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
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raalsuwaidi •
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