V36 Patches

Patches	Date
V36.2	December 11, 2024
V36.1	October 16, 2024

V36.2 Update (December 11th, 2024)

• Pipeline | Fixed an issue where intermittent and rare pipeline outages caused disruptions in the variant merge logic. No variants are missed, but customers using calling methodology in preset filters in V36.2 might be affected.

• Pipeline | Changed DRAGEN 4.3 quality thresholds for SNVs to address an issue in DRAGEN quality. DRAGEN 4.3 ML expanded ML training datasets contained errors in their truth sets, causing the ML model to lower QUAL scores on otherwise clear hom-alt calls.

  • A variant is designated as Low Quality if the VCF/FILTER is not "PASS" OR the VCF/QUAL is less than 3.

• Pipeline | Fixed an issue causing intermittent case failures in a V36 rapid pipeline component.

• Propagations from V35.5

• Organization Settings | DRAGEN arguments | Automatically converting a DRAGEN 4.2 high sensitivity setting ‘vc-enable-high-sensitivity-mode=true’ to the DRAGEN 4.3 equivalent ‘vc-enable-mosaic-detection=true’ to prevent case failure and equivalent outputs.

• Add new case | BSSH integration | Fixed an issue causing intermittent errors in VCF ingestion for customers with many BSSH projects.

• Add new case | Fixed an issue preventing adding new cases with json files.

• Pipeline | Fixed an issue that could cause duplicate variant ingestion from cases with multiple DRAGEN VCFs. The pipeline preferentially annotates the first appearance of a variant according to calling methodology rank order:

  1. "TARGETED" 2. "STAR_ALLELE" 3. "STR_REPEAT_EXPANSION" 4. "MRJD" 5. "FORCED_GENOTYPING" 6. "SMALL_VARIANT" 7. "CNV_READ_DEPTH" 8. "SV_SPLIT_END" 9. "UNKNOWN"

• Pipeline | Fixed an issue that rarely caused genome cases to get stuck in ‘In Progress’ state.

• Pipeline | Fixed an issue with missing FILTER values for trio cases.

• Pipeline | Fixed issue resulting in failed ingestion of DRAGEN targeted.json with null values.

• Analysis Tools | Visualizations | Fixed an issue where VCF track was sometimes missing from visualization.

• Versions tab | Fixed an issue where input files are sometimes missing from the versions tab.

• Propagations from v35.4

V36.1 Update (October 16th, 2024)

• Fixed an issue with the DRAGEN targeted.json caller that resulted in missing variants in a case.

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