SNVMix

SNVMix is a software tool designed to infer single nucleotide variants (SNVs) from next-generation sequencing data obtained from tumors. It uses a probabilistic Binomial mixture model to adjust for deviation of allelic frequencies in genomically unstable tumor genomes. SNVMix has three implementations that model allelic counts, nucleotide and mapping qualities of the reads, and a combination of filtering out low-quality data and probabilistic weighting of qualities. SNVMix was evaluated on 16 ovarian cancer RNASeq datasets with matched genotyping arrays and a human breast cancer genome sequenced to >40x coverage, and it outperformed competing approaches.

Topic

DNA polymorphism;Sequencing;Oncology;Statistics and probability

Detail

  • Operation: SNP detection;Filtering;Statistical calculation

  • Software interface: Command-line user interface

  • Language: ;Detects single nucleotide variants from next generation sequencing data derived from tumor tissues.;Command-line tool;C

  • License: The MIT licence

  • Cost: Free

  • Version name: -

  • Credit: The Canadian Institutes for Health Research (CIHR), the Michael Smith Foundation for Health Research (MSFHR), the Canadian Breast Cancer Foundation.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
  • Goya R, et al. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. 2010; 26:730-6. doi: 10.1093/bioinformatics/btq040
  • https://doi.org/10.1093/bioinformatics/btq040
  • PMID: 20130035
  • PMC: PMC2832826

Download and documentation

    Currently not available or not maintained.

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