Hgvs Nomenclature Lookup?

Question

[juanperin]

I hope I phrase this properly so it makes sense... I'm trying to provide annotations for indels and splice sites based on the HGVS standard nomenclature (p. etc...) Other than writing my own tool to do this, I was hoping to find a way to annotate an indel call with this p-dot nomenclature by querying a simple lookup table, or something along those lines. Or, if there is a tool out there that will convert a given index and its position etc... into the HGVS style that I'm expecting. Can't seem to find much out there about this other than the Mutalyzer tool which approaches the problem, but doesn't seem to do exactly what i want. Thanks in advance for anyone with advice in this matter. BTW. we are currently using snpEff for our annotations, however this is providing only an HGVS 'style' for SNP calls. What we really need is the HGVS style for indel and splice site calls.

Answer 1

[Jeremy Leipzig]

We have added HGVS coding DNA output to SnpEff. This fork prints HGVS for SNPs in coding regions: https://github.com/CBMi-BiG/snpEff

Answer 2

[Reece]

Also consider the Python hgvs package. [Disclosure: I'm one of the authors.] You can synthesize python objects with ref and alt variants, and stringify them into hgvs.

Answer 3

[deanna.church]

HGVS is one output of the variation reporter: http://www.ncbi.nlm.nih.gov/variation/tools/reporter You can upload your positions and allele changes to this and you should get HGVS back. If you don't get what you expect, use the 'Write to Help Desk' link at the bottom of the page and provide details about what you did and what you expect.

[deanna.church]

I actually no longer recommend using variation reporter. VEP, snpEff or Reece's hgvs package are easier to use and will give you better answers.

Answer 4

[eva.knig]

You can also use the Variant Effect Predictor (VEP) from Ensembl: http://www.ensembl.org/info/docs/variation/vep/index.html