The X_clump app identifies independent variants shared across multiple selected studies.
Before LD clumping, the app retains only variants that are present in all selected studies. You can apply a separate filter and allele-direction rule to each study before the variants are compared.
Use X_clump when you need a set of independent variants consistently represented across several studies, for example for cross-study comparison or a multi-study downstream workflow.
Before you begin
Select the studies you want to compare before launching X_clump.
The order of selected studies is important because the filters and directions fields are applied in the same order.
Name your job
Enter a descriptive Prefix. You may also add an optional Suffix to distinguish related runs.
[Screenshot 1: Highlight the Prefix and Suffix fields.]
For example:
- Prefix:
Shared_lipid_variants - Suffix:
EUR_r001
Select a project
Choose the destination project in the project_id dropdown. This is required.
[Screenshot 2: Red box around the project_id dropdown and the note directing users to Research Hub → Projects.]
The job and output files will be saved to this project.
Configure LD clumping
Set the parameters used to retain independent variants.
[Screenshot 3: Highlight the r2, MAF(LD filter), LD Ref, and padding(LD) fields.]
- r2 — The threshold used to determine whether two variants are correlated through linkage disequilibrium (LD). The default,
0.001, is stringent and retains highly independent variants. - MAF(LD filter) — The minimum minor allele frequency used for LD calculations. The default is
0.01. - LD Ref — The ancestry-specific LD reference panel. Select the reference population that best represents your study data. The default shown is EUR.
- padding(LD) — The genomic distance, in base pairs, used for LD assessment. The default is
10000.
Optionally restrict to a region
Use region to limit the workflow to a specific genomic region.
[Screenshot 4: Red box around the region dropdown.]
Leave this field blank if you want to retain eligible variants across all available regions.
Use padding(gene) to extend the region considered around genes, where relevant. The default is 0.
[Screenshot 5: Red box around the padding(gene) field.]
Apply study-specific filters
Use filters to apply a separate variant filter to each selected study.
[Screenshot 6: Red box around the filters field.]
Enter filters as a comma-separated list in the same order as the selected studies. For example, a filter may use a P-value expression such as:
pval < 5e-8
To apply no filter to a study, leave that study’s position blank while keeping the comma separators in place.
Important: The number and order of filter entries must match the number and order of selected studies.
Set allele directions
Use directions to specify whether alleles should be flipped before variants are compared across studies.
[Screenshot 7: Red box around the directions field.]
Enter directions as a comma-separated list in the same order as the selected studies:
+— Do not flip alleles before comparison.-— Flip alleles before comparison.- Leave a position blank to ignore direction for that study.
Important: The number and order of direction entries must match the number and order of selected studies.
Launch the app
Review the selected studies, project, LD settings, region, filters, and directions. Then select Launch App.
[Screenshot 8: Red box and arrow pointing to “Launch App”.]
When processing is complete, retrieve the clumped shared-variant results from the selected project or the job results area.
Tips
- X_clump only retains variants present in every selected study after the specified filters are applied.
- Confirm the selected-study order before entering filters or directions.
- Keep empty positions with commas when a study should not receive a filter or direction rule.
- Use a reference LD population that is appropriate for the ancestry represented in your study data.