Question: Plink formatting issues map file has zeros for chromosome and physical position
0
gravatar for williamsbrian5064
13 months ago by
williamsbrian5064250 wrote:

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?

ADD COMMENTlink modified 13 months ago • written 13 months ago by williamsbrian5064250

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?

ADD REPLYlink written 13 months ago by chrchang5237.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 789 users visited in the last hour