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

implement dynamic mismatch filter for long reads based on read length #96

Open
colindaven opened this issue Feb 9, 2023 · 0 comments
Open

implement dynamic mismatch filter for long reads based on read length #96

colindaven opened this issue Feb 9, 2023 · 0 comments

Comments

@colindaven
Copy link
Contributor

colindaven commented Feb 9, 2023 •
edited
Loading

see suggestions from samtools/samtools#1789

# works with samtools 1.16.1 - must upgrade samtools from 1.11

samtools view -e '[NM]/length(seq) < 0.1' test.sorted.bam | wc -l
7
samtools view -e '[NM]/length(seq) < 0.2' test.sorted.bam | wc -l
12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@colindaven