Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?

Question

[Joe Fass]

I'm looking for a general variant annotator ... one that would call a variant as synonymous, non-synonymous, non-genic, UTR, frame-shift, truncation, etc. By general I mean that we should be able to supply a reference genome sequence (fasta), gene models (say, in GFF), and vcf-formatted SNPs or indels, and that's it.

Many or all of the tools I've looked at (Annovar, Ensembl's Variant Effect Predictor, etc.) depend on an external database (i.e. NCBI or EMBL) or requires you to build a local database, or only does SNPs, or ... you get the point. We need to look at the effect of both indels and SNPs, and we cannot use one of the publicly released builds for our organism. Any takers? (thanks in advance ...)

Answer 1

[Brad Chapman]

snpEff sounds like it might fit your criteria:

http://snpeff.sourceforge.net/

It takes input as VCF files, handles SNPs and indels, and you add new genomes with a GFF description of features and fasta files:

http://snpeff.sourceforge.net/supportNewGenome.html

Pablo is very responsive to e-mails and is also on BioStar if you decide to use it and have questions.

[brentp]

i also like snpEff, but it can't handle larger indels/deletions where the variant is not encoded in the ALT column. agreed, pablo is very responsive, and he mentioned that accepting bed format may be in the pipeline which (imho) would make snpEff, more generally useful as a variant annotator.

[Brad Chapman]

Brent, thanks for the clarification; great to know. Hopefully this support will make it into a future version.

[Joe Fass]

snpEff does seem to fit the bill. Brent, the main page lists many changes for the 1.8 version, including support for pileup support (which should allow encoding of any size indel). Is your experience with snpEff prior to 1.8, or would you say there are still issues with support for large indels?

[Brad Chapman]

The latest version of snpEff was just released and has support for BED format: http://snpeff.sourceforge.net/features.html

[Brad Chapman]

The latest version of snpEff (1.9) was just released and has support for BED format: snpeff.sourceforge.net/features.html

[Liyf]

Can snpEff handle the single-mutation that does not include in any database? For example, I sequence some patients genome.

[Brad Chapman]

Yes. The effects predictions are based on the position of a mutation within transcripts, not on a pre-computed set of known mutations.

Answer 2

[Pierre Lindenbaum]

I wrote an annotator for fun: see http://plindenbaum.blogspot.com/2011/01/my-tool-to-annotate-vcf-files.html

It uses the flat files from the UCSC +biodas but it could easily be used for another source of data. In fact all you need is a collection of transcripts with:

• the genomic positions start/end of each exon
• the genomic position of the start/end of the translation
• the genomic position of the start/end of the transcription
• the genomic DNA

[User 6659]

looks interesting.

Answer 3

[alexej.knaus]

There is a open platform (www.gene-talk.com) where users can register and create an account, upload their VCF files (that will be preprocessed: annotated, etc) and even filter them.

After filtering you can take a look into existing annotation (from dbSNP, HGMD, etc.) or create your own, that would help the community of users to interpret medically relecant variants. You can comment and rank annotations and thus provide your expertise to the community.

The platfom is beeing developed at the Institute for Medical Genetics and Human Genetics at the Charité in Berlin. --> www.gene-talk.de or gene-talk.com

Answer 4

[Emily]

If you've got a genome in FASTA and a GTF file of your genes, you can build a cache to use with the VEP and don't need to use Ensembl database at all. It'll annotate any kind of variant - SNPs, indels or structural.