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This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.
CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.
The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.