SNPTools

SNPTools pipeline comprises tools for SNP analysis in next-generation sequencing data. It has an imputation engine refining raw genotype likelihoods to output high-quality genotypes or haplotypes, designed for genotyping studies of large populations. Features: 1. Addresses low coverage sequencing by using effective base depth (EBD), a nonparametric statistic; 2. A variance-based statistic, resulting in high sensitivity and specificity; 3. Employs a clustering algorithm, BAM-specific binomial mixture modeling (BBMM).

Topic

DNA polymorphism, Sequencing, Genetics, Genetic variation, DNA polymorphism

Detail

  • Operation: SNP detection › Genetic variation analysis ›

  • Software interface: Command-line interface

  • Language: C++

  • License: Other

  • Cost: Free

  • Version name: 1.0

  • Credit: Baylor College of Medicine Human Genome Sequencing Center, NIH-NHGRI, Wang Y, Lu J, Yu J, Gibbs RA, Yu F.

  • Input: -

  • Output: -

  • Contact: jy2 at bcm.ed, fyu at bcm.edu

  • Collection: -

  • Maturity: -

Publications

  • An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.
  • Wang Y, et al. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. 2013; 23:833-42. doi: 10.1101/gr.146084.112
  • https://doi.org/10.1101/gr.146084.112
  • PMID: 23296920
  • PMC: PMC3638139

Download and documentation

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