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VCF2CNA
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VCF2CNA

VCF2CNA is a tool to detect copy number variation (CNV) in Tumor/Germline Variant Call Format (VCF) files. The VCF2CNA algorithm also computes tumor purity estimates for samples.



VCF2CNA

VCF2CNA is a tool to detect copy number variation (CNV) in Tumor/Germline Variant Call Format (VCF) files. The VCF2CNA algorithm also computes tumor purity estimates for samples.

Topic

Genetics; genetic variation

Details

  • Operation: Variant detection
  • Input: VCF; Mutation Annotation Format (MAF) and the variant file format produced by the Bambino program
  • Output: -
  • Software interface: Command-line user interface; Web user interface
  • Language: R:Perl
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
    • Cost: Free
  • Version name: -
  • Credit: the National Cancer Institute of the National Institutes of Health, NCI Pan Cancer Analysis, and by the American Lebanese Syrian Associated Charities (ALSAC)
  • Contact: https://www.nature.com/articles/s41598-019-45938-x/email/correspondent/c1/new
  • Collection: -

Publications

Putnam DK, Ma X, Rice SV, Liu Y, Newman S, Zhang J, Chen X "VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity." Sci Rep. 2019 Jul 17;9(1):10357. https://doi.org/10.1038/s41598-019-45938-x
PMID: 31316100


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