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

Lancet padding analyses #11

Merged
merged 13 commits into from
Apr 14, 2020
Merged

Lancet padding analyses #11

merged 13 commits into from
Apr 14, 2020

Conversation

tkoganti
Copy link
Contributor

Analyses folder has a lancet_padding_window folder that shows how runtimes and variant results vary when using different lancet parameters (window and padding)

@tkoganti tkoganti requested a review from migbro April 13, 2020 15:24
migbro
migbro requested changes Apr 13, 2020
View reviewed changes
Copy link
Collaborator

@migbro migbro left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is quite useful - for the summary figs and the by-categroy figs, please repeat comparing consensus calls with each window size. I think that will help ascertain if and how many potentially important calls are missed.

analyses/lancet_padding_window/results/all_samples_with_var_comparison Show resolved Hide resolved
@tkoganti
Copy link
Contributor Author

tkoganti commented Apr 14, 2020 •
edited
Loading

I added consensus files and also the final plot was updated using consensus VCF files

@migbro migbro self-requested a review April 14, 2020 18:52
migbro
migbro approved these changes Apr 14, 2020
View reviewed changes
Copy link
Collaborator

@migbro migbro left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Nice work with the analysis. I feel pretty good about reducing window to 400 bp and padding to 200bp

@tkoganti tkoganti merged commit 5522c50 into master Apr 14, 2020
@tkoganti tkoganti deleted the lancet_padding_analyses branch April 14, 2020 19:07
This pull request was closed.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@migbro migbro migbro approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@tkoganti @migbro