Plink formatting issues map file has zeros for chromosome and physical position

Question

[williamsbrian5064]

Hi,

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?

[chrchang523]

Can you please post (i) the .log file from your run, and (ii) the first few columns of the first few post-header lines of test.vcf?