John Marshall

Allowing other than `Number=1` would mean that you would specify multiple failing filters as a list of comma-separated items. However the specification already describes a different way to indicate multiple...

As you allude to, it would be worth adding something like the following to §1.4.3 (“Filter field format”): > It is recommended in VCF and required in BCF that the...

> Any suggestions? Bgzip/htsfile/tabix just use `FILE`. In most cases, samtools takes SAM/BAM/CRAM interchangeably, so could just use `FILE` for this, with a note at the top of the manpage(s)...

'Tis true, there's a tension between making Usage a succinct memory jogger and being tempted to dump the whole manual page into it! Maybe it would suffice to have such...

The maintainers of these documents are familiar with Markdown.

Sure, I'll do the leg work on both. On issue #648 @yfarjoun asked for a final sign off on this (and checked if any other tags were desired) from @ilyasoifer...

See also htsget PR #430 which ran into some difficulty over the question of whether commas may appear in sample names.

Raising an issue here is the right way to get the process started. The last time we added to this list can be seen in #178 and PR #454, which...

To be honest, the actual change is trivial and we're happy to make it ourselves (add “UG (Ultima Genomics)” alphabetically; add an entry to Appendix B). And hence ideally avoid...

To summarise and expand on the discussion on slack: I think when we have discussed this issue in the past, the recommendation has been to cite the appropriate URL[^1] and/or...