Question: How to convert vcf to impute2 format?
1
gravatar for grishin
23 months ago by
grishin10
Russian Federation
grishin10 wrote:

Hi, i want to phase my data in vcf format using impute2's "-phase" option. So i tried to convert vcf file with plink:

plink --vcf data.vcf --recode oxford --out converted_data

But produced .map file does not conform to the required three-column format.
Is there any other way to convert vcf to impute2 format?

conversion impute2 vcf • 1.3k views
ADD COMMENTlink written 23 months ago by grishin10
2

Can you clarify what the problem is?  "--recode oxford" should produce a .gen file and a .sample file; this command shouldn't generate a .map file at all.

ADD REPLYlink written 23 months ago by chrchang5232.6k
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