[ensembl-dev] HGMD variations

[Will McLaren]

Hello,

Thanks for pointing out number 2 - this was indeed a bug. I'm patching
in a fix now.

Will

On 4 May 2011 08:08, Pontus Larsson <Pontus.Larsson at ebi.ac.uk> 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>
>>
>> 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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>
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