[GEN-1704] Filter out germline variants from sv files #583
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thomasyu888
approved these changes
Jan 28, 2025
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Purpose: This PR will be a hotfix to filter out germline variants from the sv file at the consortium release step (and subsequently the public release step since it just copies over the consortium release sv file) before we can release the germline variant validation rule.
Changes: Changes are isolated to the
store_sv_filesfunction indatabase_to_staging.py. Had to make it case-insensitive because I've found thatSV_STATUSis in the testing pipeline's consortium release sv file whileSV_Statusis found in the production pipeline 's consortium release sv file.Testing: Followed the standard validation of new features guide. The germline variants are filtered out.