Question: vep tabix problem
gravatar for sadri.amirhossein
20 months ago by
sadri.amirhossein10 wrote:

hi i need vep command with sift option. i used anaconda to run vep but it dosent have sift option. the installed version of vep gives me this error

MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed

i tried using containers

singularity exec ../vepsingularity/vepensemblorg.simg vep -i Final_Filter_GQ_KHUZ_MAZ_EAZ_GIL_WAZ.vcf -gff data.gff.gz -fasta GCA_003121395.1_ASM312139v1_genomic.fna --sift b

when i run this command i get this error.

Couldnt find index for file data.gff.gz at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/ line 53.
snp • 1.2k views
ADD COMMENTlink written 20 months ago by sadri.amirhossein10
 tabix -p gff data.gff.gz
ADD REPLYlink written 20 months ago by Pierre Lindenbaum129k

This was already addressed by genomax in the question your colleague mostafarafiepour asked here. Have you implemented the solution genomax gave you?

ADD REPLYlink written 20 months ago by RamRS27k
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