[ensembl-dev] variant effect predictor not reading through list of contigs?

Will McLaren wm2 at ebi.ac.uk
Fri Jun 10 09:37:01 BST 2011

Hi Mark,

Can you check that the chromosome is correctly named in your file? It
should be "MT" or "chrMT".

If you are still seeing no results it could be because the variants
are intergenic. This is a bug in the script which will be fixed for
the next release.

It may also help if you can share one or two lines of your input that
you believe should be returning results so that we can take a look
(although I note you are using a registry file, presumably this points
to a local database of yours?)


Will McLaren
Ensembl Variation

On 9 June 2011 19:34, Mark Aquino <aquinom85 at me.com> wrote:
> Hey,
> I'm having an issue getting the variant effect predictor to actually analyze my entire VCF file, for some reason it has been completely skipping entire chromosomes. notably, MT.
> My VCF is in b37 format.
> ./variant_effect_predictor.pl -i kabuki.b37.vcf --sift b --polyphen b --condel b --format vcf -r ~/script_outputs/registry.txt  -w
> -Mark Aquino
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