[ensembl-dev] mapping of variations to variation features

Andrea Edwards edwardsa at cs.man.ac.uk
Thu Feb 17 20:12:05 GMT 2011

Question 1

The following 2 human variations in dbSNP have different flanking 
sequences and are represented by different variation entries in the 
variation table. The flanking sequence of the first SNP is longer than 
the second where the overlapping regions of the flanking sequences are 
the same
-rs75478250 (vid = 18636645)
-rs28664618 (vid = 9542974)

Both of these variations have variation features affecting the locus 1:63268

How is it possible that the 2 variations  can map to the same genome 
location? I presume it is because both variations share a common length 
of flanking sequence and this common region maps to the same genomic 
DNA. What length of the flanking sequence of a variation must match the 
genomic sequence for the variation to be mapped to that genome location?

Question 2

I am have created a variation feature object for lots of SNPs and I am 
unable to get the underlying variation object. I get an error that the 
variation is undefined

my $vf = Bio::EnsEMBL::Variation::VariationFeature->new(
     -start => $pos,
     -end => $pos,
     -slice => $slice, # the variation must be attached to a slice
     -allele_string => $allele, # the first allele should be the 
reference allele
     -strand => 1,
     -map_weight => 1,
     -adaptor => $vfa, # we must attach a variation feature adap
     -variation_name => 'newSNP',

     $v = $vf->variation();
     @synonyms = @{$v->get_all_synonyms()}; <====v is undefined

I have tried this with the locus 1:63268 from above where 2 variations 
exist and I am unable to retrieve either of them. This raises this questions
a) why can't i get the variation object?
b) what happens where there is more than one variation feature entry in 
the database for the locus on which the variation feature object is 
created? Which variation feature's variation object would you return as 
the method does not return an array? E.g what variation would be 
returned for a variation feature created on locus 1:63268?

thanks very much

More information about the Dev mailing list