Angie Hinrichs

> I believe that the 585_586delins version is preferable. 585_586delins or 585_586ins? I'm confused now - for delins I think it's either Asp586delins or Asp586_Ser993delins. > This trivial case may...

Ah, interesting, thanks for the pointer. I'm hoping for something leaner than a full headless Chrome browser, so I'll have a look at the code.

> For instance, an insertion of TAG after base C at position 3 would be C3CTAG (this is example 5.2.2 from the VCF reference v4.2). My 2c: please don't follow...

@corneliusroemer Thanks so much for pointing out that inconsistency! I have changed the JSON produced by the web interface on our test server: https://hgwdev.gi.ucsc.edu/cgi-bin/hgPhyloPlace and the coloring seems to work,...

Nextstrain uses ORF1a and ORF1b, and Nextstrain is the 900lb gorilla of viral phylogenetics & visualization. :) However, the genes annotated on [RefSeq NC_045512.2](https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2) include only ORF1ab, and that is...

Biologically, as far as I know, there is no "ORF1b" transcript, only ORF1a (when transcription terminates instead of slipping & continuing) or ORF1ab (when slippage happens and transcription continues). In...

That is really strange @ktmeaton! Was the auspice JSON for your first image generated using matUtils? After using usher to add the Canadian sequences to the public tree? In your...

The sample name is taken from the corresponding column in the header's #CHROM line. Any suggestion for what to use as the sample name if there are no sample genotype...

Oh... thanks for providing the examples. So usher does not complain when there are no actual sample genotype columns, but still a GT column. But it probably does not produce...

In the meantime, in case it helps, here is a quick sed command that tacks on a sample genotype column with an arbitrary name and the first alternate allele for...