[ensembl-dev] Question Regarding VEP script warnings and --html option

Mathias Lesche mathias.lesche at biotec.tu-dresden.de
Wed Dec 11 11:14:55 GMT 2013


Dear VEP developers,

I have two questions regarding the current VEP script (Version 74).

I call the script in the following way:
/opt/rocks/bin/perl 
/projects/seq-work/user/all/vep/vep-74/variant_effect_predictor.pl -i 
input.vcf -o ouput.vcf --species homo_sapiens --fork 6 --format vcf 
--cache --dir_cache /projects/seq-work/user/all/vep/vep-cache/ --sift p 
--polyphen p --humdiv --total_length --numbers --protein --canonical 
--pubmed --gmaf --maf_1kg --maf_esp --vcf --html --offline

When running the script I get the following warning:
Use of uninitialized value $data[4] in string eq at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
415, <GEN0> line 837.
Use of uninitialized value $ref in length at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
448, <GEN0> line 837.
Use of uninitialized value $alt in pattern match (m//) at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
451, <GEN0> line 837.
Use of uninitialized value $alt in split at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
540, <GEN0> line 837.
Use of uninitialized value $alt in pattern match (m//) at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
549, <GEN0> line 837.
Use of uninitialized value $ref in concatenation (.) or string at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
621, <GEN0> line 837.
Use of uninitialized value $alt in concatenation (.) or string at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
621, <GEN0> line 837.
Use of uninitialized value $data[2] in string eq at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
621, <GEN0> line 837.
Use of uninitialized value in pattern match (m//) at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
2395, <GEN0> line 837.
Use of uninitialized value in substitution (s///) at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
2395, <GEN0> line 837.
Use of uninitialized value in string eq at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
2396, <GEN0> line 837.
Use of uninitialized value in pattern match (m//) at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
2401, <GEN0> line 837.
Use of uninitialized value in concatenation (.) or string at 
/projects/seq-work/user/all/vep/vep-74/Bio/EnsEMBL/Variation/Utils/VEP.pm line 
2402, <GEN0> line 837.

But the calculation of the variations finishes. I'm just wondering if it 
comes from the vcf file or is from the script itself.

Secondly the output.vcf.html is empty. It doesn't show the variants or 
any links to Ensembl. Is there a way to fix it? But I use the --html option.

I have to say I don't run vep on the whole vcf file. It is only a 
portion of it including the header.

Regards,
Mathias Lesche
-- 
Mathias Lesche, Dipl. Bioinformatician
Deep Sequencing Group - SFB655
c/o DFG-Center for Regenerative Therapies Dresden
Cluster of Excellence / TU Dresden
Fetscherstraße 105
01307 Dresden

Phone: +49 (351) 458 82362
Email: mathias.lesche(at)biotec.tu-dresden.de




More information about the Dev mailing list