[ensembl-dev] HGMD-PUBLIC variation set

[Will McLaren]

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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