[ensembl-dev] How can a SNP cause a frameshift mutation
Andrea Edwards
edwardsa at cs.man.ac.uk
Wed Nov 3 16:15:42 GMT 2010
Hi
I think I am doing something seriously wrong with the ensembl variation
database. I have a thousand SNPs which I am looking at, all of which are
in exons and not a single SNP according to my code is a synonymous or
non synonymous coding SNP. The vast majority of my SNPs seem to be
frameshift coding. I don't see how a SNP can cause a frameshift mutation
- only insertions and deletions can cause that.
I'd be grateful if anyone can see what I am doing wrong
#get adaptors
my $vfa = $reg->get_adaptor($species, 'variation', 'variationfeature');
my $sa = $reg->get_adaptor($species, 'core', 'slice');
my $transcript_adaptor =$reg->get_adaptor($species,
'core','Transcript');
#iterate through my SNPs
while (my $ref = $sth->fetchrow_hashref()) {
my $slice = $sa->fetch_by_region('chromosome',$ref->{'Chr'});
my $new_vf =
Bio::EnsEMBL::Variation::VariationFeature->new(
-start => $ref->{'LiftPos'}, #position of SNP
-end => $iLiftPos,
-slice => $slice, # the variation
must be attached to a slice
-allele_string => $iallele, # the first
allele should be the reference allele
-strand => 1,
-map_weight => 1,
-adaptor => $vfa, # we must attach a
variation feature adaptor
-variation_name => 'newSNP',
);
foreach $transcript_variant
(@{$new_vf->get_all_TranscriptVariations}) {
foreach $consequence
(@{$transcript_variant->consequence_type}) {
print "$consequence\n";
}
}
}
I've stripped the code right down to its minmum as shown above. Not a
single consequence is synonymous or non synonymous out of 1000 SNPs in
exons. Plenty of them are intronic but that's to be expected as SNP
might be in the exon of one gene but the intron of another.
I'm going to find all the known SNPs in my DNA of interest (cow
chromosome 7) and see what my code says when ran on known synonymous and
non-synonymous SNPs.
Any advice or help appreciated
thanks
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