Daniel Cameron

Specs-as-written, both are fine. Section 1.6.2 ``` If a field contains a list of missing values, it can be represented either as a single MISSING value (`.') or as a...

Happy with the same license as everything else.

Thanks everyone for your valued feedback. For those of you that were not able to make the GA4GH Connect session where the this VCFv4.5 release candidate 1 was presented at,...

> Therefore I would propose that that the modified base INFO field be ammended to include the intended canonical base target. ... the alternative is a database of which canonical...

> I prefer ALT as it would allow the AF, AD, ADF/ADR, etc fields to naturally represent the values we care about (like AF for modification frequency, which is obviously...

In terms of thinking of how much methylation phasing information is retained in the VCF, I'd like to propose the following thought experiment: Assume you have a perfect T2T single-cell...

> we can't have single letter codes for every type of modification as there are too many of them once we get to RNA. > There are modifications which are...

> I would personally prefer the tag in the records to be `Mm` and `Mh` for example to save some space since all the metadata about the modification is in...

>It might be common to use the suggested 5mC, 5hmC, etc, but I think it would be cleaner to remove these from the spec and allow users to specify the...

We could also allow general aliasing of ##FORMAT and ##INFO headers that seems like a large API overhead & headache for both VCF consumers and producers without much payoff other...