Verification of BALSAMIC v11.2.0

[mathiasbio]

issue: Verification of BALSAMIC v11.2.0

New release of BALSAMIC v11.2.0

Added: ^^^^^^

Changed: ^^^^^^^^

Fixed: ^^^^^^

• Adjusted bcftools somatic filter command to fix an increased amount of variants with the inclusion of triallelic sites (https://github.com/Clinical-Genomics/BALSAMIC/pull/1089)

Failing tests:

• [ ]

Tests carried out:

• [x] Containers are pulled correctly from docker hub via singularity
• [x] Reference download parallelisation works
• [x] Container download parallelisation works
• [x] Triallelic sites exists
• [x] Compression of SNV, research and clinical, VCF files
• [x] Reference files for hg38 has been updated
• [x] Somalier relatedness metric retrieval and QC pass
• [x] Somalier QC fail

Prepare for test

Prep stage

• [x] Login into hasta
• [x] paxa to balsamic-stage
• [x] Change user to HC
• [x] us
• [x] conda activate S_balsamic
• [x] pip uninstall balsamic
• [x] pip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC
• [x] Release paxa

Prep somalier failing case

• [x] Login into hasta
• [x] up
• [x] Create case:
  • [x] cg add family -a balsamic -dd scout -t 123456 cust000 SOMALIER-FAIL -> vocalgopher
  • [x] ACC11356A1 (T, male): cg add relationship -s unknown vocalgopher ACC11356A1
  • [x] ACC11286A2 (N, male): cg add relationship -s unknown vocalgopher ACC11286A2
• [x] Copy prod databases to stage:
  • [x] cg.service
  • [x] housekeeper.service
  • [x] Store tumor sample to housekeeper in stage: 'us ; cg store sample ACC11356A1'
  • [x] Store normal sample to housekeeper in stage: 'us ; cg store sample ACC11286A2'

How to test

• [x] Download containers: balsamic init --outdir /home/proj/stage/cancer/balsamic_cache --cosmic-key ${COSMIC_KEY} --genome-version hg19 --run-mode local --snakemake-opt "--cores 1 --until download_container" -r
• [x] Download reference files for hg19: balsamic init --outdir /home/proj/stage/cancer/balsamic_cache --cosmic-key ${COSMIC_KEY} --genome-version hg19 --run-mode local --snakemake-opt "--cores 30" -r
• [x] Download reference files for hg38: balsamic init --outdir /home/proj/stage/cancer/balsamic_cache --cosmic-key ${COSMIC_KEY} --genome-version hg38 --run-mode local --snakemake-opt "--cores 30" -r
• [x] livedeer (TO, WES): cg workflow balsamic start livedeer -r
  • [x] Passed QC
• [x] civilsole (TO, WGS): cg workflow balsamic start civilsole -r
  • [x] QC metrics pass (NUMBER_SITES < 50 000)
  • [x] Passed QC Except: Min requirement of 0.8 above 60x cov = 0.004532
• [x] fleetjay (TN, WGS): cg workflow balsamic start fleetjay -r
  • [x] Triallelic sites exist in SNV.somatic.fleetjay.tnscope.<research/clinical>.filtered.pass.vcf.gz
  • [x] Somalier RELATEDNESS metric is pass
  • [x] Passed QC: Except: QC metric PCT_60X: 0.00836 validation has failed. (Condition: gt 0.8, ID: ACC5821A7))
• [x] setamoeba (TO, TGA): cg workflow balsamic start setamoeba -r
  • [x] Passed QC
• [x] unitedbeagle (TN, TGA): cg workflow balsamic start unitedbeagle -r
  • [x] Passed QC
• [x] uphippo (TO, UMI): cg workflow balsamic-umi start uphippo -r --panel-bed gi_cfdna_3.1
  • [x] Passed QC Except: QC metric PCT_TARGET_BASES_1000X: 0.861996 validation has failed. (Condition: gt 0.95, ID: ACC5611A3) QC metric GC_DROPOUT: 1.650392 validation has failed. (Condition: lt 1.0, ID: ACC5611A3).
• [x] equalbug (TN, UMI): cg workflow balsamic-umi start equalbug -r --panel-bed gi_cfdna_3.1
  • [x] Passed QC Except: QC metric GC_DROPOUT: 1.087643 validation has failed. (Condition: lt 1.0, ID: ACC7363A2). (type=value_error) metrics -> 27 QC metric RELATEDNESS: -0.524 validation has failed. (Condition: gt 0.8, ID: equalbug). (type=value_error)
• [x] vocalgopher (TN, WGS): cg workflow balsamic start vocalgopher -r
  • [x] Relatedness QC check fails
  • [x] Passed QC Except: QC metric RELATEDNESS: -0.039 validation has failed. (Condition: gt 0.8, ID: vocalgopher). (as intended because it was a conscious mixup to test somalier relatedness QC check)

Review and tests:

• [x] Tests pass ---> Tests not passing
• [x] Code review
• [x] New code is executed and covered by tests, and test approve

[mathiasbio]

Deployed to production v11.2.0:

1. login to hasta
2. sudo -iu hiseq.clinical
3. up
4. conda activate P_balsamic
5. pip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC
6. balsamic --version