Hi,

I was working on converting my vcf file into plink ped/map format.

I used the following command from vcftools

    vcftools --vcf myvcf.vcf --plink --out myplink

I also would like to filter my snps based on minor allele frequency (maf).

I was wondering whether simply using

    vcftools --vcf myvcf.vcf --plink --maf 0.05 --out myplink

would do it in one step?

Or shall i do it in two steps. First convert it to the ped/map format and then use plink to do the filtering?

PLINK 1.9 can do this:

    plink --vcf myvcf.vcf --maf 0.05 --recode --out myplink

(Are you sure you want to convert to ped/map, though? PLINK prefers to work with binary bed/bim/fam.)
