[ensembl-dev] HGMD variations

Pontus Larsson Pontus.Larsson at ebi.ac.uk
Wed May 4 08:08:12 BST 2011

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

2011/5/4 Andrea Edwards <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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