Dear all,

Apologies if this does not make sense, I am very new to GWAS analysis.

I have recently imputed my data using the Michigan imputation server which has aligned my data to the HRC reference panel and has returned chr.vcf.gz and chr.info files for analysis.

I am now trying to filter to data and convert to plink bim/bed/fam files, however, my question is this. My data contains multi allelic variants and so may have duplicate ids. If I filter on MAF 0.01 using vcftools, if one of the alt variants has MAF