With

tools: vep,bcfann normalize_vcfs: true

I end up with two separate annotated VCF files,

sample.norm_BCF.ann.vcf.gz

and

sample.norm_VEP.ann.vcf.gz

. Is there a code path to merge these like with vep and snpeff?

no I don't think so. only way is to reannotate the bcf.ann files with vep in a secondary run 🫠 can you open an issue (or PR 😆)?

I'd also like to add

bcftools csq

in the near future, so perhaps the code path should go through annotation options in a defined order and then only allow one option to merge all of them? E.g. bcftools norm --> bcftools annotate --> bcftools csq --> snpeff --> ensembl-vep Otherwise dealing with all combinations would be an issue

I don’t know enough about the individual tools, but is there a reason that the annotations can’t be done in parallel and then all combined with

vcfanno

?

That might work, I don't know

vcfanno

. I know at least with

bcftools annotate

you need to know the columns to annotate with ahead of time, which might be hard to keep track of

Well if the columns are deterministic it’s relatively straightforward

the vep - snpeff combo is pretty old. @Maxime Garcia might have more context on why it is done this way

Of course, I have context