How to convert VCF file into a binary matrix to find the genotype markers

Question

[aadhirareddy1323]

Dear Friends,

I am trying to find genotype markers using 1000 Genomes VCF file for the continents Africa, Europe and East Asia. I am not sure how to convert the SNP data to a binary matrix.

Please let me know how to deal with it .

Answer 1

[andrew.j.skelton73]

I'm assuming here that you're looking for Plink format. You'll need to download the 1KG vcf file for the populations you're interested in, and then run something like:

./vcftools --vcf ./1KG.vcf --plink-tped --out plinkformat

[aadhirareddy1323]

Thank you so much for the help. I want to convert the diploid calls examples could be 0|1,1|0 and 1|2 to a matrix containing the states [(0,0),(0,1),(1,1)] respectively and the rows of the matrix should contain gene locus.

Answer 2

[stephane.plaisance]

you can also get something close to this using SNPSift (http://pcingola.github.io/SnpEff/ss_extractfields/) and export your data as a TSV table with genotypes (you may nees to simplify the genotype to get rid of ./. 0/0 0|0 or similar cases. The too allows you to keep extra VCF info in the process and can be piped to filtering steps as well.