Identification of SNPs located on genes

Question

[valerie]

Hi guys,

I have a VCF file with SNPs located on the whole genome and I want to identify those that are located on genes. I have converted VCF file to Genotype matrix and wrote a python script that goes through both GM file and GTF one to find SNPs located in genes. But this takes a huge amount of time. Does somebody know if there exists a standard tool that solves my problem in an optimal time-efficient way?

Thanks!

Answer 1

[WouterDeCoster]

If you have a VCF file then you can easily use SnpEff, Annovar or VEP for annotation.

[valerie]

Thank you for your advice! Actually my goal is to study genetic differences between two groups of mice (3 mice in each group). My VCF file contains information about all the samples. After converting to genotype matrix I selected only those SNPs that differ two groups. And now I want to understand what genes are involved in this differences. Is it possible to use the tools you mentioned to solve this problem?

[WouterDeCoster]

Most convenient would probably be to filter your vcf now with what you found when selecting variants differing between the two groups.