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PureCN

Estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection pipelines, and has support for tumor samples without matching normal samples. It integrates standard GATK-based pipelines, utilizes standard Bioconductor infrastructure for data import and export, supports both matched and unmatched samples, and was tested on targeted panels.

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PureCN versioning

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PureCN classification

PureCN specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
BAM
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
1.2.3
Requirements:
DNAcopy, VariantAnnotation
Maintained:
Yes
Interface:
Command line interface
Input data:
Already segmented data.
Output data:
A histogram of tumor vs. normal copy number log-ratios.
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable

PureCN support

Documentation

Maintainer

  • Markus Riester <>

Credits

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Publications

Institution(s)

Novartis Institutes for BioMedical Research, Cambridge, MA, USA

Funding source(s)

This work was supported by Novartis Institutes for BioMedical Research.

Link to literature

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