Question: Ensembl Variant_Effect_Predictor.Pl Raises An Error
0
gravatar for Pierre Lindenbaum
8.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

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

vcf ensembl api prediction snp • 2.3k views
ADD COMMENTlink written 8.2 years ago by Pierre Lindenbaum119k
3
gravatar for iansealy
8.2 years ago by
iansealy250
iansealy250 wrote:

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

ADD COMMENTlink written 8.2 years ago by iansealy250

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

ADD REPLYlink written 8.2 years ago by Pierre Lindenbaum119k

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.

ADD REPLYlink written 8.2 years ago by iansealy250
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