Get a table of minor an major allele from a vcf file

Question

[shinken123]

Hi

Probably this question have a simple answer but I could not find it until now. I have a VCF file that integrates the data of SNPs of 90 individuals and I would like to obtain a list that contain the ID of the SNP, the position and the mayor and minor alelle per position.

Something like this:

|    ID    | chr | position | mayor alelle | minor alelle |
|S1_10045  |  1  | 10045    |       A      |        C     |
|S1_157465 |  1  | 157465   |       C      |        G     |
|S1_267848 |  1  | 267848   |       T      |        C     |

Do you know how I could get something like this from a VCF file?

[vakul.mohanty]

You can use plink to recode the vcf file into the major minor format

[shinken123]

Ok, thank you, I will try it.

Answer 1

[alexisdereeper]

You can use the SNiPlay web application that takes VCF files as input. http://sniplay.southgreen.fr/cgi-bin/home.cgi It generates a table with this kind of information...

[shinken123]

Thank you for the information.

Answer 2

[Ram]

A VCF can give you REF and ALT alleles. These are reference alleles, which match the reference genome and the alternate alleles, which are mismatches at the position to the reference bases.

To get an idea of major and minor alleles, you will need population frequencies integrated into the analysis. Typically, a data source such as 1000 genomes or ExAC would give you the allele frequencies for the alleles at that position and you could use this information to figure out the major (AF>0.5) and minor (AF<0.5) alleles. If you restrict yourself to just the VCF file, you'd be biasing yourself based on just the samples in the VCF file.

[shinken123]

Thank you very much, I forgot to mention that the vcf file is a multisample VCF file with information from about 90 individuals.