Is possible to run VEP without consequence calculation?

Question

[magnolia]

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!

[Jeremy Leipzig]

are you running VEP with either the --cache or --offline option?

[magnolia]

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?

[Jeremy Leipzig]

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.

[magnolia]

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!

[Jeremy Leipzig]

can we see your VEP command?

[magnolia]

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,RS

[Pierre Lindenbaum]

would like to annotate my VCF with custom sources

use bcftools annotate ?

[magnolia]

I tried but if there are duplicate variants, it only annotates the first one. I tried all options for --pair-logic but 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.