[ensembl-dev] HGMD variations

Andrea Edwards edwardsa at cs.man.ac.uk
Tue May 3 23:16:24 BST 2011


I hope you all had a nice Easter break.

I'd also like to express my appreciation for the work done on the new 
variation api, documentation and VEP. It is deeply enriched.

I have a few quick questions if that is ok:

1) The human and cow variation downloads for e!62 include data for a 
table called mart_transcript_variation but the definition for this table 
is not in the sql file. Neither is this table mentioned on this page


2) Did you see this comment on biostar about a possible error in the 
VEP. I read through the VEP code and tend to agree with the OP.

3) If a variation is in dbSNP and HGMD will its source be reported as 
HGMD? There are 57930 variations in the HGMD variation set, and the same 
number of variations exist with a source of HGMD so it seems HGMD would 
trump dbSNP as the source of a variation.


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