any tools for annotating "canonical splice site variants"

Question

[CrazyB]

Similar posts have been put up in the past by other users but I haven't yet found any helpful answers.

Are there annotation tools out there that annotate variants located in the canonical splice sites? SnpEff seems to annotate them only as "intronic". Ensembl Variant effect predictor shows some annotation as "missense_variant&splice_region_variant" , but spot-checked variants do not always fall in splice regions - the documentation does not provide more info either on splice region designation.

I have a VCF with a list of 50000 variants, so am hoping to find some tools for higher-throughput annotation. Any suggestion ? Great many thanks.

Answer 1

[karl.stamm]

For canonical splice site, I suppose you mean anything within a few basepairs of an exon. Then it's easy to compute.

Get a reference of all exons (maybe from UCSC Table Browser). Reformat it to a BED file, and then with bedtools' slopBed you can make another BED file that is extended in both directions by three bp. Subtract the two (also with bedtools or bedops) and you've got now a BED file of all regions adjacent to exons. Filter your VCF to this BED by any of a thousand simple tools and you're done.

[Sleepy]

I came up with the same idea with yours. However, when I do it, I found a problem.

If an exon is the first exon of a gene, then there is no 5' splice site , if an exon is the last exon of a gene, then there is no 3' splice site. So many extended in both directions could be wrong.

I want to know if there is any suggestions to solve this.

Thank you in advance.