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.

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

Bedtools Genomecov -pc Option: Name-Sorted BAM File Error in Version 2.31.0 #1108

Open
yeeun3712 opened this issue Nov 14, 2024 · 0 comments

Comments

@yeeun3712
Copy link

I understand that the -pc option of genomecov requires a BAM file that is name-sorted.
However, I am using bedtools version 2.31.0, and I encounter the following error when using a name-sorted BAM file with the -pc option:
Input error: Chromosome chr9 found in non-sequential lines. This suggests that the input file is not sorted correctly.

On the other hand, using a position-sorted BAM file does not produce any errors, and it seems to work fine.

Is this issue related to the bedtools version?
Additionally, does using a position-sorted BAM file instead of a name-sorted BAM file produce the same results when using the -pc option in this version?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant