For better experience, turn on JavaScript!



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).


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


  • Operation: SNP detection › Genetic variation analysis ›
  • Software interface: Command-line interface
  • Language: C++
  • Operating system: Linux, Mac OS X
  • 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.
  • Contact: jy2 at bcm.ed, fyu at
  • Collection: -


Wang Y, Lu J, Yu J, Gibbs RA, Yu F "An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data." Genome Res. 2013; 23(5):833-42
PMID: 23296920
PMCID: PMC3638139

Download and documentation

If you find errors, please report here.