Choose the right tool to enrich your VCF data

A growing number of tools are available to annotate and select from VCF files. The choice of the best tool for your application depends on several factors.

when you need the job done and do not worry about the flexibility, we advise to use SnpEff and the companion SnpSift which are both easy to use java programs.

if you wish to add annotations from third-party databases that are not present in the other tools, or if you work on a organism absent from the above tool, you may consider using Annovar that was included in our former training session ([1]).

when you only need to annotate a few VCF rows, you are welcome to use public servers like:
- the EnsEMBL VEP server (introduced in our related Wiki page [2])
- the UCSC VAI ([3])
- the SeatleSeq server ([4])

Submitting 'patentable' information to the WEB infringes the novelty clause and will expose patient information to the internet, and the size of input is limited to few 100's lines

other tools have been used with success like vcfCodingSnps ([5])

Annotate your variants with SnpEff

start the SnpEff module and link to the intersect VCF file with varscan as first set

run the tool and wait for results

open the result file ending with .html

read through the extensive report and get the idea

Filter and select relevant data from a VCF file with SnpSift

SnpEff has added a large number of annotations and scores which allow us filter the data and find loci of interrest based on our assumptions. Filtering is done using SnpSift, the companion tool of SnpEff