How to interpret and extract from a Vcf file Genotype informations as values

Question

[fusion.slope]

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

[Vivek]

The correct interpretation for a diploid genome is

0/0 - 0 (Homozygous Reference)
0/1 - 1 (Heterozygous)
1/1 - 2 (Homozygous Alternate)
./. - No Data genotyped, so you'd likely skip these regions.

[Jorge Amigo]

only variants can be bi-allelic. you probably meant diploid.

[Vivek]

You're right, my bad on the terminology.

[fusion.slope]

Thanks Vivek I am working with Drosophila and I think is Biallelic.. if you know some tools to convert the information please let me know.

Tommi

[Picasa]

I don't understand what the genotype mean :

0/0 - (Homozygous Reference)
0/1 - (Heterozygous)
1/1 - (Homozygous Alternate)

1. Any clear explanation ?
2. In this exemple:

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

DGRP-038 has homozygous alternate, what does that mean?

[Vivek]

It means both chromosomes carry the insertion T>TTC

[Picasa]

HOw a mutation can be detect in the 2 chromosomes and not in 1 only ?

Answer 1

[chrchang523]

With PLINK 1.9,

plink --vcf [vcf filename] --allow-extra-chr --recode A

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

[fusion.slope]

thanks chrchang523!! ...anyway is not what I want to obtain..

[Jorge Amigo]

what exactly would you want to obtain then? the easiest way to do exactly what you describe would be to transform the vcf file into a table, using vcf-to-tab for instance, and then change the genotypes with some simple scripting.

Answer 2

[vlaufer]

vcf query from vcf tools might also work quite well for this purpose ...and I have to mention it just in case you have not already used it!