Study variation of some genes by VCF file

Question

[Zahra]

Hi all,

I want to study mutations of some genes in cancer cases and I have patients’ VCF files (I want to know what type of mutation each gene has in cohort), but I don’t know how to start for my analysis? Should I separate my interest genes from the VCF file or not? Or maybe I should filter my VCF files panel-based?

Thanks for any help or suggestion, or maybe a related paper :)

Answer 1

[Ram]

Use Variant annotation tools such as snpEff/Annovar/VEP to annotate the entire VCF file, then subset to genes of interest so you can always expand your gene list without having to re-annotate.