bio-copy-number-cnvkit-analysis

Basic Workflow

Goal: Run the complete CNVkit pipeline on a tumor-normal pair to detect copy number variants.

Approach: Execute the batch command which wraps target/antitarget generation, coverage calculation, reference building, and segmentation into one step.

## Build Reference from Normal Samples

**Goal:** Create a robust reference from pooled normal samples, then run tumor samples against it.

**Approach:** Build a panel-of-normals reference first, then batch-process tumors using the pre-built reference.

```bash

## Step 1: Build reference from multiple normals (recommended)

cnvkit.py batch \
    --normal normal1.bam normal2.bam normal3.bam \
    --targets targets.bed \
    --fasta reference.fa \
    --output-reference pooled_reference.cnn