| name | bio-workflows-cnv-pipeline |
| description | Orchestrates the copy-number pipeline from BAM to segmented, integer-called, annotated CNVs, forking on germline-vs-somatic - CNVkit (somatic exome/panel: coverage -> assay-matched reference/PoN -> fix -> segment -> purity/ploidy-aware call), GATK gCNV (germline rare-CNV cohort), and allele-specific callers (ASCAT/FACETS/PURPLE) for purity/ploidy. Use when committing the build + target/access BED + PoN once (assay-matched), building the reference from normals BEFORE segmenting, fitting purity/ploidy BEFORE integer calls in tumors, centering on the true (non-diploid) mode before GISTIC2 recurrence, or routing cfDNA to ichorCNA. Hands mechanism to the copy-number component skills; not a re-teach of any single step. |
Version Compatibility
Reference examples tested with: CNVkit 0.9.10+, GATK 4.5+ (gCNV / ModelSegments), ASCAT/FACETS/PURPLE (allele-specific), GISTIC2 2.0.23 (recurrent), ichorCNA 0.5+ (cfDNA)
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --version then <tool> --help to confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
Note: GATK gCNV runs COHORT mode (model all normals, no prior) vs CASE mode (score a singlet against a prior model) — order is DetermineGermlineContigPloidy -> GermlineCNVCaller -> PostprocessGermlineCNVCalls. Sequenza's copynumber dependency was REMOVED from Bioconductor 3.18+ (needs a fork). GATK gCNV/ModelSegments have no single method paper — cite the GATK docs. Confirm in-tool before quoting.
CNV Pipeline
"Detect copy number variants from my sequencing data" -> Fork germline-vs-somatic, commit the build + target/access BED + assay-matched reference, bias-correct against normals, segment, and integer-call off a fitted purity/ploidy.
- CLI: cnvkit target/access/antitarget -> coverage -> reference(normals) -> fix -> segment -> call (OR GATK gCNV for germline cohorts)
