Angie Hinrichs

Any plans to revisit masking? De Maio et al's collection of [Problematic Sites](https://github.com/W-L/ProblematicSites_SARS-CoV2) has grown quite a bit since initial publication. It even includes some sites contributed by my colleagues...

> B.1.526 in the US > Existing: https://nextstrain.org/ncov/north-america?f_country=USA&f_pangolin_lineage=B.1.526 with 2 tips > PR: https://nextstrain.org/staging/trial/focal-sampling/ncov/north-america?f_country=USA&f_pangolin_lineage=B.1.526 with 7 tips B.1.526 is getting more tips there -- but it's also getting placed in...

Thank you Trevor and Emma! I took a quick look at the updated builds in divergence mode, and the clades look like they're falling out in the right order [one...

Thanks! Asia looks good there but Africa got a little mixed up. See how ORF3a:Q57H (25563) compares in the two focal-sampling builds: https://nextstrain.org/staging/trial/focal-sampling/ncov/africa?gt=ORF3a.57H&m=div https://nextstrain.org/staging/trial/focal-sampling-2/ncov/africa?gt=ORF3a.57H&m=div In the first, there is one...

I think of the ambiguously placed gap as an independent variant (insGGA), which in HGVS would use the 3'-shifted location: g.73613070_ 73613071insGGA. So in my opinion, the rightmost placement of...

Thanks Reece! > with the addition that shifting should be with respect to the transcript. Even when going from c./n. to g.? (In general I would rather keep things transcript-centric...

I'll again put in a [plug](https://github.com/biocommons/hgvs/issues/514#issuecomment-415579560) for turning these ambiguous alignment regions into double-sided gaps in the alignment representation (although CIGAR might not directly support that?), and using the 3'-most...

The protein change that I get for that variant is NP_004110.2:p.Asp586delinsGlyAspArgLeuLeuArgTer . The first affected codon changes from Asp to Gly, so I believe it does need to be a...

> From the protein delins examples in the [recommendations](http://varnomen.hgvs.org/recommendations/protein/variant/delins/), this variant should be written as a position _range_. The most comparable example is `p.(Pro578_Lys579delinsLeuTer)`. Even when it's deleting (changing) a...

Thanks Reece. It's not clear to me either what would be the most correct form. I think the complete range `Asp586_Ser993` that c_to_p used to output is most informative, but...