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?