PLINK and PLINK2, AF and MAF

Question

[Sammy]

Trying to calculate MAFs for a VCF file with 40 samples, tried PLINK and PLINK2 (--freq) and the output is something like:

chr | rs code | ref allele | alt allele | MAF(plink1) or AF(plink2) | no. alleles

which is great! But some rs codes are . and don't know what variants it's referring to. The fault is obviously in the VCF file but I would like another column with the positions, is there any option I'm missing? What about ['cols='<column set descriptor>]? Not sure is what I want. Do you have any suggestions of how I can link them together?

Thanks!

Answer 1

[4galaxy77]

This is because your vcf file did not have any value in the ID column.

Run plink2 with the following flag:

--set-missing-var-ids @:#

[Sammy]

Thank you! Exactly what I was looking for!