[ensembl-dev] HGMD-PUBLIC records in Variation

Sung Gong sung at bio.cc
Tue May 24 16:30:39 BST 2011


Hi all,

Not vigorously tested yet, but some HGMD identifiers (e.g CM043264)
does not have any 'allele_string' in their variation feature object:

my $v=$va->fetch_by_name('CM043264');

foreach my $vf (@{$vfa->fetch_all_by_Variation($v)}) {
    print $vf->variation_name(), ":", $vf->allele_string(),"\n";
    print $vf->seq_region_name,":", $vf->seq_region_start,
'-',$vf->seq_region_end,"\n";
}

The script above returns:
CM043264:HGMD_MUTATION
3:8775661-8775661

Can anyone explain how the HGMD-public data is incorporated into
Ensembl human variation?

Cheers,
Sung




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