Daniel Cameron

Sorry I haven't been able to make the teleconference calls for some time. @cyenyxe is there movement on this PR/VCF 4.3?

I think we should be clear in the specifications how symbolic structural variants should be interpreted but not go as far as defining these fields for non-symbolic variants (even implicitly)....

> Strictly SVTYPE ought to be renamed TYPE to be able to cover all the types of variation I'd rather just deprecate SVTYPE. It provides no additional information over ALT...

The reserved symbolic structural variant alleles are already defined in S1.4.5. We do need to remove BND as `` was never intended to be a valid symbolic allele.

@jkbonfield I'd rather not expand this particular PR to include changes to the SAM specs themselves. My PR does appear to be highlighting some issues with SAMv1.5 that have avoided...

> The second sentence there however is broken by this example, as we go from "1" to "" back to "1". All entries are sequential positions, with "" being an...

Sorry for the delay. Grant season just ended so I'll be able to get these done over the next week or two. @tskir Do we have a offical location for...

#553: removing SVTYPE makes this synchronisation simpler.

See #448 for an example of how real-world tools are using fields in a non-compliant manner to work around the lack of proper subclonal support.

I've now stripped the bit where DUP subtypes defined different breakpoints than the root types. This badly breaks backwards compatability and can be better handled as part of the `EVENT`/`EVENTTYPE`...