Setting an outgroup for the "Dengue virus DENVx genotypes" dataset #67
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
j23414
changed the title
j23414
changed the title
j23414
force-pushed
the
nextclade-genotype-set-outgroup
branch
2 times, most recently
from
d317d0e
to
03277a4
Compare
genehack
approved these changes
Jun 20, 2024
|
Merging this so I can continue working on feedback from slack in a new issue and PR. |
Adds the reconstructed root of the All serotype tree as an outgroup for the DENVx trees.
j23414
force-pushed
the
nextclade-genotype-set-outgroup
branch
from
03277a4
to
d3c39c7
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
This pull request aims to fine-tune the Dengue virus Denv* (
dengue/denv*) datasets for accurate genotype-level assignment. Similar to a previous PR (#58) for the Dengue virus All (dengue/all) dataset, it addresses the issue of cross-serotype samples being falsely assigned to genotypes within a specific serotype. For example, when querying all samples against a DENV4 dataset, there were false-positive "DENV4II" genotype calls.To resolve this issue, the following actions were taken, inspired by a suggestion from @rneher in a Slack channel:
clades_genotype.tsvfile by serotypeResults
The resulting trees with minimized cross-serotype false-positive genotype-level assignments are documented in #69
Related issue(s)
Checklist
The dataset has been pushed to PR nextstrain/nextclade_data#203 and is available for testing at the links in the PR comment nextstrain/nextclade_data#203 (comment)