Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Split-read SV calling improvements #15

Merged
merged 49 commits into from
Oct 25, 2024
Merged

Split-read SV calling improvements #15

merged 49 commits into from
Oct 25, 2024

Conversation

jonperdomo
Copy link
Collaborator

@jonperdomo jonperdomo commented Apr 12, 2024 •
edited
Loading

Improvements to split-read SV calling:

  • Read sequences are not aligned multiple times. We choose the best sequence based on mismatch rates, and trim the other sequence
  • Only the highest probability SV is kept when comparing copy number prediction in split alignment regions

Also added an ethnicity argument for gnomAD allele frequencies, and fixed errors insertion and duplication breakpoints

@jonperdomo jonperdomo linked an issue Apr 12, 2024 that may be closed by this pull request
Add SV scoring model #1
Open
@jonperdomo
Copy link
Collaborator Author

Distribution of scoring values for HG002 SVs from model trained on HG002 SV gold standard:
Distribution of score values for HG002 SVs with logreg model trained on Truvari TP and FN

jonperdomo added 24 commits April 24, 2024 15:28
@jonperdomo
Increase cnv detection threshold
5219bf4
@jonperdomo
Fix duplication end positions
7dcec51
@jonperdomo
Fix duplication vcf format for annovar
10c1428
@jonperdomo
Fix off-by-one dup and ins length error
e6ef22d
@jonperdomo
Update README.md
9b304f3
@jonperdomo
Work on adding hmm likelihood as support
1e19485
@jonperdomo
Update probability ranges
9e1475a
@jonperdomo
Fix likelihood error
e80413b
@jonperdomo
Update scikit version and implement HDBSCAN clustering
e99916e
@jonperdomo
Update style
8650dd2
@jonperdomo
Fix alternate allele error, improve clustering
f0f2fe1
@jonperdomo
Update merge support
ff3b47d
@jonperdomo
Work on merge
30bca88
@jonperdomo
Fix error
471810a
@jonperdomo
Fix hmm score parsing bug
8f36c3b
@jonperdomo
Update merge support algorithm for dels, ins, dups
c6f7631
@jonperdomo
HMM prediction tests
bc4177a
@jonperdomo
Fix log2 division by zero error
7d51830
@jonperdomo
Remove cnv tests for now
6b264ac
@jonperdomo
Add more hmm documentation
6d5bd3e
@jonperdomo
Fix HMM indexing errors
87b3164
@jonperdomo
Fix conda YML and update input SNPs vector
d94aecd
@jonperdomo
Remove python version
e095393
@jonperdomo
Remove hmm testing code and comments
d907ba7
@jonperdomo jonperdomo removed a link to an issue Oct 21, 2024
Add SV scoring model #1
Open
@jonperdomo jonperdomo changed the title Add initial scoring model Split-read SV calling improvements Oct 21, 2024
@jonperdomo jonperdomo marked this pull request as ready for review October 21, 2024 18:59
@jonperdomo jonperdomo marked this pull request as draft October 21, 2024 18:59
@jonperdomo jonperdomo marked this pull request as ready for review October 25, 2024 16:21
@jonperdomo jonperdomo merged commit 2812c1e into main Oct 25, 2024
1 check passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@jonperdomo