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

Duarte Molha duartemolha at gmail.com
Tue May 17 09:15:54 BST 2011


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

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