Individual skill
copy-number-variation
Copy-number variant analysis — detection from sequencing/arrays, segmentation, and clinical interpretation.
skills/copy-number-variation/SKILL.md
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## Overview
copy-number-variation covers detecting deletions and duplications from genomic data: read-depth
methods for WGS/WES, SNP-array approaches (BAF/LRR), segmentation algorithms, and interpreting
CNVs for rare disease and cancer. CNVs are a major cause of Mendelian disease and a key somatic
alteration class — but detection is noisier than SNV calling and interpretation leans heavily on
population databases.
## When to use
- Germline CNV calling from WES/WGS: read-depth methods (GATK gCNV, CNVnator, Manta).
- SNP-array CNV analysis: PennCNV, LRR/BAF interpretation.
- Somatic copy-number in cancer: FACETS, ASCAT (purity/ploidy-aware), GISTIC for recurrent
regions.