feat: Release v15.0.0 #1422
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feat: Release v15.0.0 #1422
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#### Added - high_normal_tumor_af_frac filter in bcftools for TNscope WGS T+N analysis, and UMI T+N analysis which allows for 30% of tumor in the normal. #### Removed - alt_allele_in_normal set by TNscope for WGS T+N analysis, and UMI T+N analysis
### Added - new option for exome samples --exome with modified bcftools filters compared to standard targeted workflow ### Changed - reduced stringency of targeted none-exome bcftools filters for min MQ - removed -u flag from VarDict T+N and T only rules ### Removed - removed -U flag to VarDict T+N rule to start calling SVs in VarDict (required for FLT3)
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1422 +/- ##
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Coverage 99.44% 99.44%
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Files 40 40
Lines 1983 1994 +11
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+ Hits 1972 1983 +11
Misses 11 11
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This was referenced Mar 22, 2024
#### Removed - bcftools filter command keeping only PASS and triallelic-sites as the initial step of quality-filters
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ivadym
approved these changes
Apr 10, 2024
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Description
This is a relatively small update to Balsamic with some significant changes to VarDict filters and settings, which influences all TGA workflows and in particular exome-analyses, as well as a new feature with a custom solution for detecting IGH::DUX4 rearrangements in WGS.
Added
Changed
Removed
Pre-Validation Checklist
Before proceeding with the validation process, ensure that the following tasks have been completed:
Install Balsamic in stage and production environments in hasta and build its cache.
BALSAMIC release_v15.0.0branch, from the instructions given above:sudo <...>tmux new -s <...>pip uninstall balsamicpip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC@release_v15.0.0balsamic init --out-dir <STAGE_PATH> --account <...> --cosmic-key ${COSMIC_KEY} --genome-version hg19 --cache-version 15.0.0 --run-mode local --snakemake-opt "--cores 40" -rbalsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key ${COSMIC_KEY} --genome-version hg38 --cache-version 15.0.0 --run-mode local --snakemake-opt "--cores 8" -rbalsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key ${COSMIC_KEY} --genome-version canfam3 --cache-version 15.0.0 --run-mode local --snakemake-opt "--cores 8" -rConfirm the availability of necessary resources, such as test cases.
(Made script to verify this automatically: /home/proj/stage/cancer/validation/scripts/verify_presence_of_test_cases.sh)Review the changelog and ensure all changes and updates are documented:
Set up the stage environment with the necessary software and configurations:
Workflow integrity results
Workflow Integrity Verification Cases
More details here: https://docs.google.com/spreadsheets/d/1p4-oGUs7YDfRjZjqnIHqrC1ryg7C2TOLNpWBDEdwGxA/edit#gid=0
Hg38 integrity verifications:
Put failed case here: validation/15.0.0/failed_integration_tests
Made bug-report here: #1425
Release specific integration verifications:
Storage, Delivery and Upload Integrity Verifications
Validation and implementation plan status
Pull-request for validation-report made here:
https://github.com/Clinical-Genomics/validations/pull/177
Pull-request for implementation-plan here:
https://github.com/Clinical-Genomics/validations/pull/178