PureCN

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.

Topic

Genetics;sequencing;DNA structural variation

Detail

  • Operation: Sequence classification;Copy number estimation

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.14.1

  • Credit: Novartis Institutes for BioMedical Research.

  • Input: -

  • Output: -

  • Contact: markus.riester@novartis.com

  • Collection: BioConductor

  • Maturity: Stable

Publications

  • PureCN: copy number calling and SNV classification using targeted short read sequencing.
  • Riester M, et al. PureCN: copy number calling and SNV classification using targeted short read sequencing. PureCN: copy number calling and SNV classification using targeted short read sequencing. 2016; 11:13. doi: 10.1186/s13029-016-0060-z
  • https://doi.org/10.1186/s13029-016-0060-z
  • PMID: 27999612
  • PMC: PMC5157099

Download and documentation

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