Fix variant id harmonization and NA handling in summary stats and LD#413
Merged
danielnachun merged 10 commits intoStatFunGen:mainfrom Nov 6, 2025
Merged
Fix variant id harmonization and NA handling in summary stats and LD#413danielnachun merged 10 commits intoStatFunGen:mainfrom
danielnachun merged 10 commits intoStatFunGen:mainfrom
Conversation
Contributor
|
Thank you @kal26 ; @danielnachun could you review and decide if we should merge it? I have not seen issues in this patch |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
I added some checks to ensure consistent naming between the individual data, summary stats, and LD. I also filter out NA values in sum stats which cause colocboost errors. The
colocboost_analysis_pipelinecan now run with the variant ID formats in my GWAS and LD data.