domains / families / science / cnv-pipeline

cnv-pipeline

separate

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.

When to use

• Orchestrating copy-number pipeline from BAM to annotated CNVs
• Forking germline vs somatic workflows
• Committing build, target/access BED, and assay-matched reference
• Building reference from normals before segmenting
• Fitting purity/ploidy before integer calls in tumors
• Centering on true mode before GISTIC2 recurrence
• Routing cfDNA to ichorCNA
• Managing hand-offs to copy-number component skills

When not to use

• Re-teaching the mechanism of any single step
• Teaching internals of component skills

Skill page

Source