[ensembl-dev] Getting SNP information from location. Bug?

Will McLaren wm2 at ebi.ac.uk
Thu Mar 27 12:13:25 GMT 2014


Hi Alexia,

This SNP has been flagged as suspect by our QC process, as indicated by the
info box of the page you linked to.

By default the API does not return these flagged variants; you can force
the API to return them by calling the following:

$vfa->db->include_failed_variations(1);

before you do the fetch.

You only need to do this once; the flag is set and retained in memory for
all variation adaptors that you use.

Regards

Will McLaren
Ensembl Variation


On 27 March 2014 12:01, Alexia Cardona <ac812 at cam.ac.uk> wrote:

> Hi,
> I am trying to get SNP information given a location on the genome.  I am
> basically creating a slice from a location (Chromosome 1 pos 564598) and
> use it to get the list of variant features in that slice
> (fetch_all_by_Slice).  The problem is that the array is empty.  When
> searching through Ensembl browser online however there is SNP at that
> location.  Does anyone know if this is a bug or if I'm doing something
> wrong please?
>
> (Code snipped below)
>
> Thanks
>
> Ensembl link online:
> http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=1:564098-565098;v=rs144350286;vdb=variation;vf=4442009
>
> ##############################
>
> use strict;
> use warnings;
>
> use Bio::EnsEMBL::Registry;
>
> my $registry = "Bio::EnsEMBL::Registry";
>
> $registry->load_registry_from_db(
>   -host => 'ensembldb.ensembl.org',
>   -user => 'anonymous',
> );
>
>
> #create slice
> my $sliceAdaptor = $registry->get_adaptor('human', 'core', 'slice');
> my $slice = $sliceAdaptor->fetch_by_region('chromosome', 1, 564598 ,
> 564598);
> my $vfa = $registry->get_adaptor('human', 'variation', 'variationfeature');
> my$vfs = $vfa->fetch_all_by_Slice($slice);
> print scalar @$vfs; #returns 0
> my $vfs2 = $vfa->fetch_all_somatic_by_Slice($slice);
> print scalar @$vfs2; #returns 0
>
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