[ensembl-dev] identifying known variants that map to multiple genome locations

[Andrea Edwards]

Esteemed api developers,

Is there any easy way with the perl api to tell if a known variant (by 
this i mean one that has a an rsID and that i have created like this:

# Variation feature representing a single nucleotide polymorphism
$vf = *Bio::EnsEMBL::Variation::VariationFeature*->new
(-start => 100,
-end => 100,
-strand => 1,
-slice => $slice,
-allele_string => 'A/T',
-variation_name => 'rs635421',
-map_weight => 1,
-variation => $v);

is known to map to another region of the genome other than the region 
have specified with the slice/start/end properties?

dbSNP variants can be assigned to multiple genome locations when it 
hasn't been possible to unambiguously assign them to a single location.

If i can't tell from the variation feature directly i believe i can do this:

$vfa = $reg->get_adaptor("human","variation","variationfeature");
$va = $reg->get_adaptor("human","variation","variation");

# fetch all genome hits for a particular variation
$v = $va->fetch_by_name('rs56');
$count =  @{$vfa->fetch_all_by_Variation($v)}
if $count > 1 then it maps to more than one place?

I was hoping to be able to do it directly from teh variation feature

thanks

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