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

Regional plots with LD #83

Open
xEmz opened this issue Mar 21, 2024 · 1 comment
Open

Regional plots with LD #83

xEmz opened this issue Mar 21, 2024 · 1 comment

Comments

@xEmz
Copy link

xEmz commented Mar 21, 2024

Hi Yunye,

I want to make regional plots with LD (using the hg19 vcf) in GWASLAB. However, this seems to take forever to run. Do you know how this can be sped up?

Kind regards,
Emma
@Cloufield
Copy link
Owner

Hi Emma,
I am wondering if tabix is avaialble in your environment path? GWASLab will use tabix if available in environment path.
If not, it will just iterate through the entire VCF file, which might be extremely slow if the VCF is large.

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
@Cloufield @xEmz