v5 freq ht generation #720
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- Create annotations directory structure for v5 - Add main frequency calculation script with differential analysis approach - Support for both gnomAD and All of Us datasets - Framework for identifying samples to remove due to relatedness/ancestry changes - Age histogram calculation functionality - Resource management and pipeline structure
…ry change detection - Add coverage data integration using AN from coverage computation - Implement ancestry change detection between v4 and v5 - Add comprehensive documentation in README.md - Enhance sample identification logic for both gnomAD and All of Us datasets - Add error handling for missing resources - Support for ancestry change frequency calculations - Improve resource management and pipeline structure
…ling and AoU processing - Refactor process_gnomad_dataset to handle consent sample withdrawals by subtracting frequencies from v4 freq table - Implement efficient AoU processing using variant_data + all-sites AN approach - Add comprehensive utility functions and checkpoints for performance - Integrate FAF, grpmax, and age histogram calculations - Add group membership resource integration for both gnomAD and AoU datasets - Include robust error handling and logging throughout pipeline
…ataset is being used
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