vep can't find index file

[jerrypgreenberg]

Hi,

I have a user at SDSC (www.sdsc.edu) who is trying to run vep.

She did some runs with a vep I built for her , but then ran into a problem with a job where it couldn't find Tabix.pm (even though executing perl -e "use Bio::DB::HTS::Tabix" did not give any errors ; (perl 5.28.1))

this was with vep 112 (our cluster runs rocky 8 linux)

I then converted the vep docker file to a singularity image (vep 113), ( because of security issues , we cannot run docker) downloaded homo_sapiens_vep_113_GRCh38.tar.gz and tried it again with the following command (where "vep" is a shell in which the singularity image is called):

vep -i VEP_input_CodingGenes.vcf --cache --transcript_version --vcf_info_field CSQ -o VEP_output_CodingGenesv26_hgvs.vcf --custom gencode.v26.annotation.gtf.gz,GENCODE,gtf

and it gave the following error message:

Couldn't find index for file gencode.v26.annotation.gtf.gz at /usr/local/lib/x86_64-linux-gnu/perl/5.34.0/Bio/DB/HTS/Tabix.pm line 53.

Ill be glad to provide any files you might need.

Thanks and please forgive my ignorance: Im a chemist, not a geneticist.

Jerry Greenberg
SDSC User Services

[jamie-m-a]

Hi @jerrypgreenberg

Sorry you've been having trouble with your VEP install, with regard to the first problem, it can be the case VEP sometimes can't see the system tabix (as it usually tries to install it's own). It can be tricky to debug so going down the route of using the containerised version is often simpler - which is what you've done.

For the second problem it's hopefully just a simple issue of an index not existing for that GTF - can you confirm whether there is a gencode.v26.annotation.gtf.gz.tbi file present? If not it can be generated like so:
tabix -p gff gencode.v26.annotation.gtf.gz

[jerrypgreenberg]

I ran that via the container and got the following error:

tbx_index_build failed: gencode.v26.annotation.gtf.gz

Thanks,

Jerry

[jamie-m-a]

Hi @jerrypgreenberg

Possibly the file is gzipped rather than bgzipped? Tabix requires bgzip's blockwise compression for indexing. Can you try unzipping the file and recompressing with bgzip, then rerunning the tabix command.