I have a vcf file that I am converted into ped and map files for plink. When I look at the map file that plink creates, it has zeros for chromosome and physical position. I can seem to figure out why or any documentation on plinks website. This is what I am running
plink --vcf test.vcf --recode --vcf-half-call reference --dog --out test
I am not sure how to fix this.. maybe a different --recode?