[ensembl-dev] HGMD variations

Andrea Edwards edwardsa at cs.man.ac.uk
Wed May 4 13:34:20 BST 2011


Thanks for your reply. I have not received any emails from Rhoda or Beth 
in relation to my original post about the extra table. Was there perhaps 
a problem with the mailing list recently? I didn't receive any messages 
for a couple of days but I assumed it was Easter break. I seem to be 
getting them now again as I have received your's and will's emails today.

  I Have searched the archives and can see the posts there though.


On 04/05/11 08:08, Pontus Larsson wrote:
> Hi Andrea,
> 1. This is a production table that was mistakenly included in the 
> dump. Please see Rhoda and Beth's answers to your original post.
> 2. I will leave it to Will to answer this fully but I believe this has 
> to do with the way indels are specified in the VCF file format.
> 3. Since HGMD do not disclose the alleles of their variations to us, 
> we cannot merge HGMD variations with co-located variations from dbSNP 
> or any other source. Thus, these will be listed as co-located (rather 
> than synonyms) and will not mask or replace dbSNP as the source of the 
> variation.
> Hope this helps
> /Pontus
> 2011/5/4 Andrea Edwards <edwardsa at cs.man.ac.uk 
> <mailto:edwardsa at cs.man.ac.uk>>
>     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
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