Entering edit mode
5.5 years ago
sadri.amirhossein
▴
10
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/Tabix.pm line 53.
