vep tabix problem
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2.4 years ago

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.
SNP • 1.8k views
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 tabix -p gff data.gff.gz
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This was already addressed by genomax in the question your colleague mostafarafiepour asked here. Have you implemented the solution genomax gave you?

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