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

kook.dev at free.fr kook.dev at free.fr
Tue Feb 19 16:09:59 GMT 2013


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.

Sébastien Letort - bio-informaticien

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