[ensembl-dev] VEP.pm Can't locate object method "get_all_StructualVariationOverlaps"

Michael Yourshaw myourshaw at ucla.edu
Wed May 23 22:32:53 BST 2012


With Ensembl version 67, cvs download 2012-05-22 and VEP v 2.5, I’m getting an error in VEP.pm

The offending input VCF record:
22      22517055        MERGED_DEL_2_105173     A       <DEL>   .       .       AN=2184;ERATE=0.0099;RSQ=0.6595;CIEND=-17,33;THETA=0.0005;AVGPOST=0.9871;AC=24;END=22599640;VT=SV;CIPOS=-18,19;SVTYPE=DEL;LDAF=0.0155;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01   GT:AB:AD:DP:GQ:PL       0/1:0.88:36,5:41:77.58:78,0,611 1/1:.:0,5:5:12.01:111,12,0

The error:
	Can't locate object method "get_all_StructualVariationOverlaps" via package "Bio::EnsEMBL::Variation::StructuralVariationFeature" at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1214, <GEN9> line 66.

The line of code:
    foreach my $svo(@{$svf->get_all_StructualVariationOverlaps}) {

The fix would be:
	 foreach my $svo(@{$svf->get_all_StructuralVariationOverlaps}) {




ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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