[ensembl-dev] Variants seq_region_name excluding patches / seq_region_start for VCF

Genomeo Dev genomeodev at gmail.com
Wed Dec 17 18:03:45 GMT 2014


*Using Ensembl 75 VM*

I am trying to retrieve coordinates and sequence regions for some variants
using variant IDs:

my $var = $var_adaptor->fetch_by_name('rs7904594');
my $vfeatures = $var->get_all_VariationFeatures();
while (my $vf = shift @{$vfeatures}){
print $vf->seq_region_name(), "\t", $vf->seq_region_start(), "\n";


1. Is there a way I can choose to print main chromosomes only excluding
2. I want to use the position information in a VCF. seq_region_start only
works for SNPs. How can I make use of that for indels?


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