Petr Danecek

This is just a practical decision to avoid the complexity of parsing of the many GFF flavors that exist out there. Ensembl's human GFF is one of the most frequently...

The only code made publicly available I am aware of is here https://github.com/samtools/bcftools/issues/1208#issuecomment-620642373. I'd be very happy to host a `gff2gff` script in `bcftools/misc` but cannot commit to developing it...

This script has been now added, thank you @flashton2003

There were some fixes recently, can you try with the latest github version and if the problem persists, provide a small test case to reproduce the bug? http://samtools.github.io/bcftools/howtos/install.html

You can check if the chromosomes are in single blocks with something like ``` bcftools query -f'%CHROM\n' file.bcf | uniq -c ``` Most likely not a problem with bcftools.

Since this is not a bcftools problem, I am closing the issue

The VCF specification does not say, the interpretation is up to the user (i.e. the VCF creator). The most sensible interpretation is to treat `.` as every other missing value...

@nh13 that's correct, the missing value `"."` should not be interpreted one way or another.

Most likely the VCF is not well formatted, with the latest version an informative error message should be printed. Which version of bcftools are you using? Try if the sample...

Hi, sorry for the delay about this. The code as it is currently written does not allow to distinguishes well between genotypes that are 'consistent' and have 'missing information but...