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
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 https://doi.org/10.1101/gr.146084.112
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