<div dir="ltr">Hi,<div>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?</div>
<div><br></div><div>(Code snipped below)</div><div><br></div><div>Thanks</div><div><br></div><div>Ensembl link online: <a href="http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=1:564098-565098;v=rs144350286;vdb=variation;vf=4442009">http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=1:564098-565098;v=rs144350286;vdb=variation;vf=4442009</a></div>
<div><br></div><div>##############################</div><div><br></div><div><div>use strict;</div><div>use warnings;</div><div><br></div><div>use Bio::EnsEMBL::Registry;</div><div><br></div><div>my $registry = "Bio::EnsEMBL::Registry";</div>
<div><br></div><div>$registry->load_registry_from_db(</div><div> -host => '<a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a>',</div><div> -user => 'anonymous',</div><div>);</div>
<div>
<br></div><div><br></div><div>#create slice</div><div>my $sliceAdaptor = $registry->get_adaptor('human', 'core', 'slice');</div><div>my $slice = $sliceAdaptor->fetch_by_region('chromosome', 1, 564598 , 564598);</div>
<div>my $vfa = $registry->get_adaptor('human', 'variation', 'variationfeature');</div><div>my$vfs = $vfa->fetch_all_by_Slice($slice);</div><div>print scalar @$vfs; #returns 0</div><div>my $vfs2 = $vfa->fetch_all_somatic_by_Slice($slice);</div>
<div>print scalar @$vfs2; #returns 0</div></div></div>