Currently, VEP allows to use VCF input with only the first 5 fields, leaving the remaining 3 mandatory fields as NULL.
However, for SVs, VEP tries to do a string comparison on the INFO field, resulting in the warnings:
Use of uninitialized value in pattern match (m//) at /hps/software/users/ensembl/variation/nuno/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 340.
Use of uninitialized value in pattern match (m//) at /hps/software/users/ensembl/variation/nuno/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 359.
Use of uninitialized value in pattern match (m//) at /hps/software/users/ensembl/variation/nuno/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 378.
Use of uninitialized value in pattern match (m//) at /hps/software/users/ensembl/variation/nuno/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 397.
The solution is to simply complete SV information by appending . to the 3 last mandatory fields.
Testing
The results should be exactly the same (but should not show a warning) for all formats regardless of using 5 or 8 fields in VCF input:
Currently, VEP allows to use VCF input with only the first 5 fields, leaving the remaining 3 mandatory fields as
NULL.However, for SVs, VEP tries to do a string comparison on the
INFOfield, resulting in the warnings:The solution is to simply complete SV information by appending
.to the 3 last mandatory fields.Testing
The results should be exactly the same (but should not show a warning) for all formats regardless of using 5 or 8 fields in VCF input: