Does anyone know of a reliable workflow to convert traditional/deprecated HGVS variants such as "HBB:IVS2+705T>G" to genomic coordinates or current Sequence Variant Nomenclature (http://varnomen.hgvs.org)?
I'm aware of the hgvs
and pyhvgs
Python packages, but those don't understand the deprecated notation.
Many thanks!
Try ensembl variation api
I'm not aware of a tool for the depecrated notations. Whatever tool you use you have to be aware that the result could be ambiguous as the hgvs notation depends on the transcripts and of course one gen can have multiple ones.
@finswimmer Thank you, maybe I should've been more explicit.
The HGVS Recommendations (https://www.hgvs.org/mutnomen/disc.html#tradition) say this about traditional descriptions:
The problem is that there are still a lot of resources out there that use this notation, e.g. DBASS (http://www.dbass.org.uk), but also more recent papers: https://rdcu.be/7nT9.
Of course what's even worse is that some of these resources don't specify the transcript ID they're referring to, but only the gene name. The best way to deal with this is probably just to use the canonical RefSeq transcript.
Hello hannes,
I know these recommendation and I fully support the opinion not to use things like
IVS+
. Without knowing the transcript it is much harder to find the genomic the position.I fear one have to write a program that first find all possible positions for the given transcripts of a gene, filter out those where the reference bases doesn't much. If you have luck there will be only one result left.
(Nice excercise. Maybe I have some time next week to do something with python ...)
fin swimmer