Support for annotations in table format

[edg1983]

Hi,

Any plan to add support for annotations coming in a table format so that they can also be converted to gnotate format and used during variant filtering? Indeed, several genome-wide mutation impact predictions come in tab-separated files.

I appreciate that we can annotate the file before with vcfanno and then filter with slivar using the pre-annotated fields, but annotation with slivar is faster and could be convenient to do the whole process in a single step.

[brentp]

i understand why this would be useful, but i don't intend to add--mostly so slivar doesn't get so complex that i can't maintain (but also so that users can't use it) originally, slivar wasn't going to have the gnotation piece, but annotating with gnomad as so critical for rare-disease stuff that I had to add it. I don't want to push that to far as vcfanno (which is quite good IMO) has shown how hard it is for me to maintain and users to understand when all use-cases are supported. plus, the main advantage of slivar gnotation (speed) is only realized on huge datasets like gnomad.

that said, it's possible to convert any tab-delimited file into a VCF and then use make-gnotate to convert it to a gnotation zip file.