Next Gen Sequenced Snp Annotation

Question

[Travis]

Hi all,

I am aware of the SNPeff program which seems to extract Ensembl annotation (location and predicted effect) for SNPs in NGS data but I am wondering if there is anything else available - for example something that might determine whether a polymorphism is known/novel or determine its frequency in the population.

Does anything like this exist or would it be necessary to create scripts that would for example compare to dbSNP for uniqueness and the 1000 genomes project for frequency.

Best,

Gavin

[Pablo]

I can add that functionality to SnpEff if you want.

[Pablo]

OK, I'll do it.

[Travis]

Sounds like a great idea!

[Travis]

Thanks a lot - much appreciated!

Answer 1

[Jorge Amigo]

I'm sure there will be some more out there, but some options I've come across are the following:

• ANNOVAR, a set of local scripts that download for you the databases you may need for your annotations, allowing fast retrieval of information. we are currently configuring and evaluating it, as it seems very interesting for high production environments. you may want to read their NAR paper to know more about it.
• SeattleSeqAnnotation, a web site where you can upload your variants and you'll easily retrieve a large number of annotations. this tool has been already referred in some papers, although no paper has been yet published describing it.
• Ensembl's Variant Effect Predictor, both a web tool (limited to 750 variants) and a perl script that will also allow you to deeply characterize your variants, always performing the queries against remote Ensembl. I personally like this one, but it doesn't seem to provide dbSNP ids.