[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
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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