Daniel Cameron

>Does the VCF standard support fields that are vector of Strings? I couldn't find anything in the spec related to this topic. Yes. See http://samtools.github.io/hts-specs/VCFv4.3.pdf section 1.6.1.8: `INFO - additional...

> (I.e. Do you want to keep the mapping quality from before you clipped it?) In this particular instance, it's bwa reporting a 50S50I alignment, I'm cleaning up the start/end...

>The reason is that $ is such a special character that it was not expected to be inside any search. I tried to see if there was an alphabet option...

Those fields are sufficiently restricted that percent encoding is both unnecessary and would itself introduce invalid characters. We should probably explicitly restrict info and format field percent encoding to string...

It's a bit unclear on what the values can/should be. I presume an array of 3 booleans would be `0,1,1` with 0=FALSE, 1=TRUE, but the PR should explicitly state that...

> @d-cameron mentioned in one of the conversations that there's a need to have a notation for NOT phase-set, meaning that one can tell that a particular allele is NOT...

Resurrecting this issue to incorporate into 4.4 and the fact that bundles aren't well defined has finally come up (#643) . The plan is: - Break BCF partial phasing; use...

>In the point 1, I don't understand the proposal to disallow multiple ALT alleles in gVCF fields and this would not be a good thing. I should have been clearer....

Having now implemented this into the dev branch of `StructuralVariantAnnotation` I think we should keep both `CILEN` and `CIEND`. It does mean that records can be inconsistent, but it allows...

`END` clarifications now included in VCF4.4