[ensembl-dev] VEP: reporting HGVS identifiers with RefSeq accessions
reece at harts.net
Tue Feb 14 06:44:00 GMT 2012
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
- 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.
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