Version Compatibility

Reference examples tested with: CNVkit 0.9+, Ensembl VEP 111+, GATK 4.5+, SnpEff 5.2+, bcftools 1.19+, picard 3.1+

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.

Somatic Variant Pipeline

"Call somatic mutations from my tumor-normal pair" → Orchestrate alignment, Mutect2 somatic calling, contamination filtering, variant annotation (Funcotator/VEP), TMB calculation, and mutational signature analysis.

Complete workflow for calling somatic mutations from tumor-normal paired samples.

Pipeline Overview