NCI-CGR / GwasQcPipeline

The CGR GWAS QC processing workflow.
https://nci-cgr.github.io/GwasQcPipeline/
MIT License
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Checkpoint prevents populations with >50 cases or controls but <50 cases and <50 controls running HWE #295

Closed kliao12 closed 3 months ago

kliao12 commented 3 months ago

Checkpoint population_controls_checkpoint identifies populations with # cases > 50 or # controls > 50. Misses populations with >50 cases or controls (e.g. 30 cases, 30 controls).

kliao12 commented 3 months ago

Discussed on 6/6/24 to fix faulty checkpoint to create for pops with >50 controls or > 50 cases + controls.

Update QC reports and documentation.