Hi!

I have to perform eQTL analysis and now I have to manipuate the vcf file. I would like to know if there are some way to convert these information: `1/1=2` ; `./.=0` ; `0/1=1`)

Example:

    #CHROM  POS     REF     ALT     DGRP-038        DGRP-040        DGRP-045
    2L            2262     T          TTC     1/1:7:0               ./.:0:0              ./.:0:0

Then in this case the following:

    #CHROM  POS     REF     ALT     sample-1        sample-2        sample-3
    2L            2262     T          TTC           2                   0                   0

Are there any software to do that?

The second question is: does the meaning of these values (0 1 2) are the following?

 - reference/reference (no mutation) = 1 no present in my example
 - reference/alternative (1 mutation copy) = 2 and in my case (1/1:7:0 )
 - alternative/alternative (both copy mutated) = 0 and in my case (./.)

Thanks in advance!!  
Tommi
<p>With PLINK 1.9,</p>

<p><code>plink --vcf [vcf filename] --allow-extra-chr --recode A</code></p>

<p>will write 0/1/2-coded genotypes to plink.raw .</p>
