cwhelan

Just wanted to alert whoever looks at this that @vruano started to work on this and ended up wanting to refactor the `Allele` class. A lot of that work is...

@d-cameron Added a few comments on places that I think could use clarifications -- sorry that I didn't make them sooner. Again, thanks for spearheading this change.

>Tools based on micro-array or copy number evidence report DUP as an a region of elevated copy number (typically +1 copy). They are making a claim about the number of...

@rhdolin > Doesn't PRECISE/IMPRECISE achieve what INFO.SVBKPT would? (Although I've seen examples that are both PRECISE and have CIPOS and CIEND, which I find confusing). Usually IMPRECISE is only used...

@d-cameron I think my top preference from your list is your option 4: Keep DEL / DUP ambiguous but add an INFO field indicating whether there's a breakpoint claim of...

One more comment on CNVs: cohort-based CNV callers can disentangle different copy number variable alleles even without breakpoint evidence. For example, in the case of overlapping duplications with clearly different...

It seems to me like @bhandsaker 's use cases shake out like this with respect to this pull request: 1. This is incompatible with the proposed changes since it can...

@d-cameron Thanks for your answer. >CN:x is still allowed, it just has undefined semantics and is not considered a "non-structural symbolic allele". We just need to remove this phase and...

@tskir Unless I'm misunderstanding, under your proposal a bi-allelic or rare duplication discovered by a read depth-based method would have to be represented by `SVTYPE=CNV`, an `ALT` of ``, and...

I'll also add a vote in favor of clarifying in the spec that the tags shouldn't be ordered -- I don't really think the order of the keys should matter...