The problem: I have a VCF file, a reference genome, and a bunch of annotations for the reference (genes, repeat regions, etc.) as GFF or BED files.
What I would like is a tool that takes all of this as input and outputs a tab- or comma-delimited table containing as much information as possible. Potential columns in the output include:
- Type of variant (SNV, structural, etc)
- Details of variant (e.g. reference base, variant base, coverage, position, etc)
- Annotations overlapping variant
- Annotations near variant (e.g. is it just upstream of a gene)
- If it appears in a coding region, does it change the amino acid.
There are many tools that do something like this. But to the newbie (like me) it is not clear which tools are worth starting with. Since the majority of tools take a little effort to get working in the first place, my question is:
What tool comes closest to doing what I have described, is known to reliable, and is likely to be maintained for the next few years.