Ensembl Variant_Effect_Predictor.Pl Raises An Error

Question

[Pierre Lindenbaum]

Hi all,

I'm trying to use the varianteffectpredictor.pl to analyse the content of a VCF file produced by mpileup/bcftools.

It raised an error when a insertion was submitted. My minimal input raising an error is:

echo -e 'chr1\t10000\t.\tT\tTA' | ./variant_effect_predictor.pl --format vcf

-------------------- EXCEPTION --------------------
MSG: Start must be less than or equal to end+1
STACK Bio::EnsEMBL::Feature::new /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Feature.pm:139
STACK Bio::EnsEMBL::Variation::VariationFeature::new /home/lindenb/tmp/ENSEMBL/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm:177
STACK toplevel ./variant_effect_predictor.pl:309
Ensembl API version = 61
---------------------------------------------------

what's the problem ? Should I remove all the indels from the VCF ?

Thanks,

Pierre

Answer 1

[iansealy]

Try doing a cvs up. I think Will fixed this bug yesterday:

http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/scripts/examples/variant_effect_predictor.pl?root=ensembl&r1=1.2.2.1&r2=1.2.2.2

[Pierre Lindenbaum]

whoooo, thanks Ian ! I'll validate your answer as soon as the perl source will be released in the zip archive.

[iansealy]

If you download http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation.tar.gz?root=ensembl&only_with_tag=branch-ensembl-61&view=tar then that should be up to date.