Angie Hinrichs

I'm realizing now that I did a 180 on on reference-backfilling in deleted regions: first I said > in the worst case, they may backfill with reference bases (a horror...

I did a quick test of branch specific masking -- files are in [test_files_added.tar.gz](https://github.com/yatisht/usher/files/10671390/test_files_added.tar.gz). I made a script maskDeletions.sh which is like my maskDelta.sh, but only the deletions, and only...

(and of course I'd like to know if tweaking the MSA fasta so that deletions are forced to reference instead of N has a similar structural effect on the tree...

FYI since there have been other questions about masking recently e.g. #324 I replaced the bash script (maskDelta.sh) with a YAML description of branches and masked sites/ranges/reversions: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml (and a...

+1 Thanks @theosanderson for the heads-up. Anecdotally, I've seen a few other sets of adjacent (or at least close) mutations that cause trouble in the Omicron branches of the tree,...

Hi @LiXingguangBrandonStark -- I haven't used mask_alignment_using_vcf.py nor did I write it (from github history it looks like @conorwalker is the main author), but if you cd to the ProblematicSites_SARS-CoV2/src/...

In case it's of any use, here's my script that fetches all metadata and uses GenBase's API to download (one at a time unfortunately) the sequences that I don't already...

Ah, I missed your explanation in #8 while I was writing in #4! Makes sense, and hopefully the mutation frequencies are not a hard requirement in virus_properties.json because I can...

Here is a python snippet that fetches my [nextstrain.clade-mutations.tsv](https://github.com/ucscGenomeBrowser/kent/raw/master/src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv) from github and overwrites ./virus_properties.json with its mutations: ``` import re import requests import json props = { "schemaVersion": "s2r 0.0.1",...

Just for fun I also tried making virus_properties.json from [pango.clade-mutations.tsv](https://github.com/ucscGenomeBrowser/kent/raw/master/src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv) and adding a line for each AY.* lineage to mapping.csv but it didn't work for this example, even with `--unique...