How to annotate a VCF and convert it to a list of genes (names) with defined mutations?

Question

[flight22121]

How to annotate a VCF and convert it to a list of genes (names) with defined mutations? What software and approach is rational?

[mks002]

Variant Studio gives good result Variant Studio. Otherwise go with SNPeff.

Answer 1

[agata88]

I am using SnpEff and SnpSift for annotation. It has also option to convert results in tab format (SnpSift.jar extractFields).

Best,

Agata

Answer 2

[Chun-Jie Liu]

The ANNOVAR has a lot of annotation method. You may check the link.

Answer 3

[Denise CS]

Try the Ensembl Variant Effect Predictor. It will predict the consequence of the variants in your VCF and give the genes where the variants map to. In addition, you will get many other features such as whether the variant falls in a TFBS motif or not, whether it's pathogenic according to ClinVar or not, the frequency of the alleles in both 1000 genomes and ExAC populations, and loads more. The script version of the VEP also contains several plugins for getting the CADD score and many more.