[ensembl-dev] VEP Gene strand

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Mon Jan 26 11:26:18 GMT 2015


Hi,

I'm working on a plugin for VEP script.
Usually in "run" fucntion I use a code like this to get the variant chr, 
position, ref allele and var allele.

my $line = 
$vf->{base_variation_feature_overlap}->{base_variation_feature}->{_line};
my @split_line = split ("\t", $line);
$chr = $split_line[0];
$pos = $split_line[1];
$ref_allele = $split_line[3];
my $var_allele = $line_hash->{Allele};

However for this plugin I need information about Gene in this position, 
in particular the Gene strand.

Is this possible to retrieve from any vep object?

Thanks!

Best regards,
Guillermo.
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