Petr Danecek

Hi, yes, that's correct. This has not been done for the case when annotating from a VCF yet

The VCF specification allows to drop sample's trailing FORMAT fields (case 2), but it also allows to use a single MISSING_VALUE as an abbreviated way of expressing how many missing...

Maybe it should, but it does not have to. HTSlib reads in VCF, internally converts the trailing missing fields to `.`, then outputs it as `MISSING_VALUE,END_OF_VECTOR`, for both VCF and...

This is easy to add in principle, the only question is what the syntax would look like. Maybe use the `@` symbol which is already used to reference a file...

Sorry about the poor documentation, clearly something for us to improve. What version of bcftools are you using? This should tell the program to calculate the allele frequencies from the...

These are valid VCF lines and the program treats such records as any other. What kind of functionality do you have in mind specifically? The short answer is that none...

GFFs provided by Ensembl use this convention `ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/`

I am open for this to be changed as long as it continues working with Ensembl files. A more general (and also an easier) solution might be to provide a...

There are too many possible variations a GFF can have, I don't want to burden `bcftools csq` with that complexity. I will accept a pull request that extends the `https://github.com/samtools/bcftools/blob/develop/misc/gff2gff.py`...

Phase is 8th column of GFF https://www.ncbi.nlm.nih.gov/datasets/docs/reference-docs/file-formats/about-ncbi-gff3. The program detected some inconsistency between expected and observed phase (frame).