Daniel Cameron

Not that anyone except me actually uses it, but VCF already refers to an external file in the ##assembly header*. Technically ##contig as well but that's an input file so...

Closing since VCF field encoding allows this to be done but we have no intention to add HTTP-style Content-Type metainformation.

At the next file format meeting we should decide on a policy on how far we backport clarifications and how we want to balance specifications stability, maintenance burden, and specifications...

I've some time to review the proposal and I can see a number of issues with SV support, many of which are also problems for VCF. Here is my take...

I'm a bit confused as to what is actually being represented by a gene fusion variant. Are we referring to the transcript-level products, or the breakpoint(s) in the underlying DNA...

Apologies that I was not able to make the call. From my perspective, we need to two-level model (I'm working on one for VCFv4.3) that separates the low-level claims made...

We now have our preprint up: https://www.biorxiv.org/content/10.1101/781013v1 @reece we now proper documentation for our circos plots https://github.com/hartwigmedical/hmftools/blob/master/sv-linx/README_VIS.md#circos-panel as well as our event classifier/DNA-Seq fusion caller https://github.com/hartwigmedical/hmftools/tree/master/sv-linx @ahwagner The NCI fusion...

Here's another read-world example that I don't think the proposed design handles:  In this sample, we see a chromoplex event causing a TMPRSS2-ERG fusion via PTEN itron 1 (follow...

@bpitel12 how do you find that notation scaling? From the looks of it, the detailed notation requires ~40-60 characters per breakpoint (rearrangements using the nomenclature of the linked paper).. A...

> I mean, such a Cicos plot is drawn from individual events, isn’t it? It's from individual breakpoints and (allele-specific) copy numbers. 'event' is a loaded term. In my work,...