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PureCN package is for detection of copy number variation (CNV) and single nucleotide variation classification in targeted sequencing data. The PureCN algorithm estimates tumor purity, CNV, loss of heterozygosity (LOH), contamination, and classifies single nucleotide variants (SNVs) by somatic status and clonality. The algorithm integrates well with various somatic variant detection pipelines.


Genetics; sequencing; DNA structural variation


  • Operation: Sequence classification; Copy number estimation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Artistic License 2.0
  • Cost: Free
  • Version name: 1.14.1
  • Maturity: Stable
  • Credit: Novartis Institutes for BioMedical Research.
  • Contact: markus.riester _at_
  • Collection: BioConductor


Riester M, Singh AP, Brannon AR, Yu K, Campbell CD, Chiang DY, Morrissey MP "PureCN: copy number calling and SNV classification using targeted short read sequencing." Source Code Biol Med. 2016 Dec 15;11:13. eCollection 2016.
PMID: 27999612
PMCID: PMC5157099

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21.
PMID: 25633503
PMCID: PMC4509590

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.
PMID: 15461798
PMCID: PMC545600

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