[ensembl-dev] Retrieving a slice of GL*** Chromossomes

Will McLaren wm2 at ebi.ac.uk
Tue May 17 09:32:21 BST 2011

Hi Duarte,

You should be able to retrieve a slice using the following code:

my $slice = $slice_adaptor->(undef, "GL000224.1");



On 17 May 2011 09:15, Duarte Molha <duartemolha at gmail.com> wrote:
> Hi
> I have modified your script VarianEffectpredictor to obtain some additional
> information when analyzing vcf files.
> For that I obtain a splice of the region where a variation is and then do
> some analysis of the features in that region.
> It works fine for all variations on regular chromosomes but it fails for
> haplotype sequences such as features that map to say GL000224.1.
> When I create a slice for that region the slice object returns undef.
> However the variant effect predictor script is able to retrieve transcripts
> for those regions.
> Can we work with these alternative regions in the same way as with correctly
> assembled HG19 chromosomes?
> Best regards
> Duarte
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