[ensembl-dev] possible VEP bug

[Fiona Cunningham]

Hello Sarah,
I think you have the most recent  HGVS knowledge. Does what he says
makes sense? What happens to HGVS when you are on the opposite strand?
Presumably it is all relative to the transcript.?
Fiona

-----------------------------------------------------------------------------------
Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org || www.lrg-sequence.org
fiona at ebi.ac.uk   || t: +44 1223 494612




---------- Forwarded message ----------
From: Michael Krauthammer <michael.krauthammer at yale.edu>
Date: 21 March 2012 01:25
Subject: [ensembl-dev] possible VEP bug
To: dev at ensembl.org


A possible (small) VEP bug report:

The HGVS input parser does not seem to check for the directionality of
the transcript

The following (correct) input:

CCDS6119.1:c.3327+1G>C

results in error.

The following (wrong) input works:

CCDS6119.1:c.3327-1G>C

The output of above input results in

CCDS6119.1:c.3327-1G>C  8:41552109      C       CCDS6119.1
CCDS6119.1      Transcript      splice-5        -       -       -
 -       -       -
ENSP=CCDS6119.1;HGVSc=CCDS6119.1:c.3327+1G>C;INTRON=28/41

Nota bene: GVSc=CCDS6119.1:c.3327+1G>C  (!) which is the correct notation.

Michael Krauthammer

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