Extract codon information from VCF file

Question

[k.rajain1212]

I have VCF file of Bos Taurus. I want to get the codons of SNP as well as know the region i.e if they lie in intronic region or exonic. Can anyone name any good tool or a package in R which can do my job.

[finswimmer]

Hello,

you could use ensembl's VEP for that as an online tool.

If you prefer local installation have a look at SnpEff.

fin swimmer

Answer 1

[NB]

Try VariantAnnotation