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

bwa ALT supplementary reads not handled correctly. #363

Closed
d-cameron opened this issue Jun 8, 2020 · 1 comment
Closed

bwa ALT supplementary reads not handled correctly. #363

d-cameron opened this issue Jun 8, 2020 · 1 comment
Labels
enhancement

Comments

@d-cameron
Copy link
Member

bwa violates the same specs for ALT contig alignments. Need to add special case code to identify the actual chimeric alignments from the secondary alignments which bwa reports as supplementary.
@d-cameron
Copy link
Member Author

See lh3/bwa#282

@d-cameron d-cameron mentioned this issue Feb 9, 2021
Closed
d-cameron pushed a commit that referenced this issue Feb 22, 2021
Updated ComputeSamTags behaviour
c051fae 
- Dropping excessively overlapping split read alignments (contained alignment & >25bp overlaps)
- #282 Add summary stats to ComputeSamTags/PreprocessForBreakendAssembly output
- #363 preferring non-ALT alignments when determining best split reads
- Refactored SAMRecordUtil.calculateTemplateTags into multiple methods
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@d-cameron