Question: Plink formatting issues map file has zeros for chromosome and physical position
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gravatar for williamsbrian5064
21 months ago by
williamsbrian5064320 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 21 months ago • written 21 months ago by williamsbrian5064320

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 21 months ago by chrchang5237.7k
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