[ensembl-dev] Fwd: Possible bug in variation API - result different from VEP

[Bhavana Harsha]

I forgot to mention that these are GRCh37 coordinates.

Bhavana

Begin forwarded message:

From: Bhavana Harsha <bh4 at sanger.ac.uk<mailto:bh4 at sanger.ac.uk>>
Subject: Possible bug in variation API - result different from VEP
Date: 11 July 2017 at 14:17:20 BST
To: dev at ensembl.org<mailto:dev at ensembl.org>

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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