Is possible to run VEP without consequence calculation?
Hi,
I would like to annotate my VCF with custom sources. I don't need any other information about the variants.
Is it possible to run VEP to annotate with custom sources only, without VEP's sources?
The reason why I want this is because annotation takes too long so I'm thinking it would run much faster this way.
Thank you!
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magnolia •
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are you running VEP with either the --cache or --offline option?
I have both in my command. I'm thinking if I didn't have them, VEP would connect to Ensembl which would make everything worse. Is that wrong?
sounds correct. I think it's better to look at your VEP command rather than try to reinvent things. The annotation shouldn't take longer than upstream steps.
Hmm, alright. Maybe my expectations were unnecessarily high? :) I'll try to subset my annotation sources and try that way then. Thank you so much!
can we see your VEP command?
Sure:
vep -i $path2vep_input --offline --fork 8 -o $path2txtout \ --tab --cache --dir_cache $path2cache --cache_version $cacheVersion --force --allow_non_variant --show_ref_allele --assembly $assembly --fields Uploaded_variation,Location,REF_ALLELE,Allele,dbSNP_RS,ClinVar_ALLELEID,ClinVar_CLNSIG --custom $path2clinvar,ClinVar,vcf,exact,0,ALLELEID,CLNSIG --custom $path2dbsnp,dbSNP,vcf,exact,0,RSuse bcftools annotate ?
I tried but if there are duplicate variants, it only annotates the first one. I tried all options for
--pair-logicbut nothing worked. Also, it annotates all variants regardless of genotype. VEP on the other hand doesn't annotate 0/0. I know I can filter out after bcftools but just saying.