[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
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