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

Will McLaren wm2 at ebi.ac.uk
Tue May 17 09:33:01 BST 2011


That should have been:

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

Itchy trigger finger :-)


On 17 May 2011 09:32, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Hi Duarte,
> You should be able to retrieve a slice using the following code:
> my $slice = $slice_adaptor->(undef, "GL000224.1");
> Cheers
> Will
> 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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