<p>Hi, i want to phase my data in vcf format using impute2&#39;s &quot;-phase&quot; option. So i tried to convert vcf file with plink:</p>

<pre>
plink --vcf data.vcf --recode oxford --out converted_data
</pre>

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

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.