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

[William McLaren]

Hi Bhavana,

I’m unable to replicate this issue. I’ve run your code (slightly modified to dump out the results, exact code at the end of this mail), and this is the result I see:

$VAR1 = [
  'ENSP00000352610.4:p.Ala307ThrfsTer41',
  'ENSP00000269305.4:p.Ala307ThrfsTer34',
  'ENSP00000398846.2:p.Ala307ThrfsTer32',
  'ENSP00000391127.2:p.Ala307ThrfsTer40',
  'ENSP00000391478.2:p.Ala307ThrfsTer34',
  'ENSP00000425104.1:p.Ala175ThrfsTer?'
];

Double check that your API (both ensembl and ensembl-variation) is up to date for release/89.

Regards

Will McLaren
Ensembl Variation


###
use Bio::EnsEMBL::Registry;

my $reg = 'Bio::EnsEMBL::Registry';

$reg->load_registry_from_db(-host => 'ensembldb.ensembl.org', -species => 'homo sapiens', -user => 'anonymous', -port => 3337, -db_version => 89);
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;

use Data::Dumper;
$Data::Dumper::Maxdepth = 3;
$Data::Dumper::Indent = 1;
print STDERR Dumper \@hgvsp;

On 11 July 2017 at 15:24:39, Bhavana Harsha (bh4 at sanger.ac.uk) wrote:

I forgot to mention that these are GRCh37 coordinates.

Bhavana

Begin forwarded message:

From: Bhavana Harsha <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

Hello, 

For the following variant
17 75769157577019 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', -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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