[ensembl-dev] HGMD variations

[Andrea Edwards]

Hello

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

http://www.ensembl.org/info/docs/variation/variation_schema.html

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.
http://biostar.stackexchange.com/questions/7781/problem-with-ensembl-variant-effect-predictor-stand-alone-perl-tool/7921#7921

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.

cheers