[ensembl-dev] VEP: reporting HGVS identifiers with RefSeq accessions

[Reece Hart]

Greetings-

I'm using VEP 2.3 with Ensembl 65. I'd like to report HGVS tags with
RefSeq NM accessions rather than ENST accessions where such is
consistent with the ENST-based prediction. I'm also fetching SIFT and
PolyPhen predictions, so I can't use --refseq.

Has anyone already written a plugin to tackle this?

If not, I'm going to give this a shot. I'd appreciate comments about
the following approach.

In plugin new():
- get an adaptor for otherfeatures transcripts.

In plugin run():
- Identify the otherfeatures transcript that best corresponds to the
ENST.  I'm concerned about differences in exon structure.  Is it
sufficient to look for otherfeatures transcripts by xref, or do I need
to compare exon structures (up to the variant, anyway)?

- Construct a new TranscriptVariationAllele using the RefSeq
transcript. I can use the same slice and compute relative transcript
offsets, right?

- Call hgvs_coding, _protein, etc. on the new TVA

I have a table of the discordance between RefSeqs and GRCh37. I would
probably post process with that, but I could put it in the plugin too.


Is that about right? Thanks for tips.


Thanks,
Reece