[ensembl-dev] HGMD-PUBLIC variation set

[Will McLaren]

Apologies yes it should have read

$vf->feature_Slice

Will

On Tuesday, 13 September 2011,  <cj5 at sanger.ac.uk> wrote:
> Hi Will,
> Thanks for the reply.
> Can I ask about the solution below - isn't the slice to which a variation
> feature is attached an arbitrary slice, often the whole chromosome?
> This being the case, when we call
> $vf->adaptor->fetch_all_by_Slice($vf->slice) don't we get back more than
> we need? Shouldn't we just be looking for colocated variants in a minimal
> slice corresponding to the variant location?
>
> Thanks
> Chris
>
>> Hi Chris,
>>
>> We used to "merge" HGMD-PUBLIC variants with dbSNP variants where they
>> were co-located, such that the HGMD identifier became a synonym of the
>> dbSNP variant.
>>
>> We stopped doing this in release 62 since the HGMD and dbSNP
>> identifiers may not actually represent the same genomic change. I'm
>> assuming the variant you have is one of those into which an HGMD
>> identifier was merged.
>>
>> All members of the HGMD-PUBLIC set (renamed to 'HGMD-PUBLIC phenotype
>> variants') are now variants with HGMD identifiers as their primary
>> identifier.
>>
>> You can find if a dbSNP (or other) variant is co-located with a HGMD
>> variant using something like the following:
>>
>> foreach my $colocated_hgmd_vf(grep {$_->source =~ /HGMD/}
>> @{$vf->adaptor->fetch_all_by_Slice($vf->slice)}) {
>>    ....
>> }
>>
>> Hope this helps
>>
>> Will McLaren
>> Ensembl Variation
>>
>> On 13 September 2011 15:24,  <cj5 at sanger.ac.uk> wrote:
>>> Hi,
>>>
>>> Could somebody please advise why the following code no longer picks up
>>> the
>>> HGMD-PUBLIC Varation set when I change from Version 61 to 62?
>>>
>>>            my $vf = $tv->variation_feature();   # $tv = Transcript
>>> Variant
>>>            my $var = $vf->variation();
>>>            my @vs = @{$vs_adaptor->fetch_all_by_Variation($var)};
>>>            foreach my $vs (@vs) {
>>>
>>>                if ($vs->name() =~ /HGMD-PUBLIC/) {
>>>                    ....
>>>                }
>>>            }
>>>
>>>
>>>
>>> Many Thanks
>>> --
>>> Chris Joyce
>>> Wellcome Trust Sanger Institute
>>>
>>>
>>>
>>>
>>>
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>>
>
>
>
>
> --
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