[ensembl-dev] VEP : bug on some 1kG data with "--filter" option

[Will McLaren]

Hello,

Thanks for the bug report.

I've put a fix for this into the CVS server - you'll need to update your
ensembl-variation module.

Regards

Will McLaren
Ensembl Variation


On 19 February 2013 16:09, <kook.dev at free.fr> wrote:

> Hello,
>
> I tried variant_effet_predictor.pl (downloaded from CVS) on some VCF file
> that come from 1000 Genome project.
>
> Here is my command line :
> perl variant_effet_predictor.pl -i bug.vcf --filter no_coding --format vcf
>
> where bug.vcf contains
>
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
> 22      16942585        esv2678061      C       <DEL>   .       PASS
>  AC=21;AF=0.01;AFR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.9870;CIEND=-65,88;CIPOS=-76,81;END=16945887;ERATE=0.0010;EUR_AF=0.01;LDAF=0.0129;RSQ=0.6112;SVTYPE=DEL;THETA=0.0026;VT=SV
>
> program ends with :
> 2013-02-19 16:46:10 - Calculating consequences
> Can't locate object method "consequence_type" via package
> "Bio::EnsEMBL::Variation:tructuralVariationFeature" at
> /PROGS/lib/ensembl-variation/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1947,
> <GEN0> line 2.
>
> Everything is ok if I do not use the --filter option.
>
> regards,
> Sébastien Letort - bio-informaticien
>
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