Daniel Cameron

> is there any point in requiring any ordering at all The reason I proposed an ordering was for round-trip stability. Different tools will output headers in different order which...

@mbaudis Doesn't the interpretation of the meaning of DUP depend on what is defined in the sample GT field? I would interpret `, SVCLAIM=CN GT=1/2` as a copy number neutral...

VCF phasing can be made explicit by using a `|` or `/` suffix and this functionality is needed to be able to phase a haploid variant with other non-haploid variants....

I can see two scenarios for phased haploid calls: 1) copy number loss causes a non-haploid region to become haploid. The caller can chose whether or not the overlapping deletion...

>I'd clarify whether it's required to include SVLEN for BND records, and also explicitly state what SVLEN should be for intra-chromosomal BND records. Already done as part of #468

`` should not be a valid ALT allele.

There was discussion back in the middle of last year on the VCFtools-spec mailing list regarding allowing INFO/FORMAT fields to represent strings with reserved characters. A number of escape/encoding schemes...

> We already specify a scheme for % encoding of reserved characters. Would that be sufficient to insert a json blob into an info field? Yes. Whether it gets nicely...

Or turn this issue into a discussion on whether we want to add first-class support for JSON or XML through the addition of relevant INFO Type fields. If we're adding...

Honestly, I don't think gene or transcript level annotations of any sort belong in VCF. VCF has no concept of genes or transcripts. A set of record-level annotation of the...