[ensembl-dev] Possible bug in variation API - result different from VEP
Bhavana Harsha
bh4 at sanger.ac.uk
Tue Jul 11 14:17:19 BST 2017
Hello,
For the following variant
17 7576915 7577019 TGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACC/- +
the correct protein consequence for the transcript ENST00000269305 should be
ENSP00000269305.4:p.Ala307ThrfsTer34
As is confirmed by the VEP web interface, REST API and the VEP perl script.
However, when I try to get this using the Variation API, I get
ENSP00000269305.4:p.Ala307Thr
This is how I’m using the API:
$reg->load_registry_from_db(-host => 'ensembldb.ensembl.org<http://ensembldb.ensembl.org>', -species => 'homo sapiens', -user => 'anonymous', -port => 3337);
my $sa = $reg->get_adaptor(‘human’, 'core', 'slice');
my $vfa = $reg->get_adaptor('human', 'variation', 'VariationFeature');
my $slice = $sa->fetch_by_region(‘chromosome', 17);
my $vf = Bio::EnsEMBL::Variation::VariationFeature->new(-start => 7576915, -end => 7577019, -slice => $slice,
-allele_string => ‘TGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACC/-‘, -strand => 1, -adaptor => $vfa);
my $cons = $vf->get_all_TranscriptVariations;
my @hgvsp = grep { defined } map { $_->hgvs_protein } map { @{$_->get_all_alternate_TranscriptVariationAlleles} } @$cons;
I’m using v89 for the API and the VEP script.
Is there something I’m doing wrong in my script?
Cheers,
Bhavana
---------------------------------------------
Bhavana Harsha
Bioinformatician
COSMIC
Wellcome Trust Sanger Institute
Hinxton, UK
CB10 1SA
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