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

numerically sort positions in vcfs #290

Open
arkal opened this issue May 26, 2018 · 2 comments
Open

numerically sort positions in vcfs #290

arkal opened this issue May 26, 2018 · 2 comments

Comments

@arkal
Copy link
Collaborator

arkal commented May 26, 2018

No description provided.

davidstew pushed a commit that referenced this issue Jun 5, 2018
sort output vcf positions numerically (resolves #290)
4a2d984 
resolves #290

outputted vcfs after merging are sorted chromosomes 1..22,X,Y,M
and positions within are sorted numerically.
@hbeale
Copy link

hbeale commented Sep 17, 2019

It appears that this issue is still outstanding. When I tried to use bcftools isec on a protect-generated vcf (the snpeffed one), I got the following error message:

[E::hts_idx_push] Unsorted positions on sequence #1: 102527054 followed by 10259505
tbx_index_build failed:

@arkal
Copy link
Collaborator Author

arkal commented Sep 18, 2019

Looks like this was made on an issues branch but was never committed to master..... i'll get to this later today!

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
2 participants
@hbeale @arkal