Structural annotations of vcf. files

Question

[Lukáš]

Is it possible to pick subfields from structural annotation like ANN field by SNPEFF, VEP ENSEMBL with one tool?

I am just asking, because i have vcf. with multiple anotations like ANN field annoted by SnpEff. However i am not capable to extract specific subfields from the fiels.

I tried pick the subfield in simular way to picking TAG from info field, but it only pick whole field. I found SnpSift Extract field, but because the vcfs have diffent annotatins (many can be picked by bcftools query).

But when i tried to find option how to pick all subfields from secondary annotations field with regular options like #CHROM i I was not able to find a specific way how to do it.

[Ram]

You've explored both available options - annotation-tool specific scripts such as SnpSift Extract (plus filter-vep for VEP) and a completely generic tool (bcftools query). I don't think there exists any middle ground as it is not worth the effort combining existing tools and dealing with mixed annotation sources. You should just use the annotation-tool specific scripts and combine compatible tab-delimited files.

Another option might be MAFtools - I know it supports ANNOVAR, but I'm not sure it can work with snpEff or VEP.

[Lukas]

Thank you. At least I finally know, that I am trying to find something which probably even doesn't exist.