Variant Annotation

Question

[Chethana]

Hello,

I have a VCF file, and I have converted it into data frame. Now I have to do gene annotation, but the vcf file has #chrom pos ref alt columns. like there is no genomic coordinates (i.e. start and end). Now I have to add gene annotation based on the #chrom and pos.

I have been trying using different R packages, I'm getting lot of errors.

Please suggest some ideas. Or are there any packages, so I can do the analysis?, Preferably in R programming language.

[iraun]

If you want to annotate the variants from your VCF file, e.g., determine the effect or impact of those variant in the resultant gene products, you could directly use VEP, using as input the VCF file. Alternatively, SnpEff is also another popular annotation tool.