An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.

@article{Wang2013AnIV,
  title={An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.},
  author={Yi Wang and James Lu and Jin Yu and Richard A. Gibbs and Fuli Yu},
  journal={Genome research},
  year={2013},
  volume={23 5},
  pages={833-42}
}
Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of populations, implemented in a pipeline called SNPTools. Our pipeline contains several innovations that specifically address challenges caused by low-coverage population sequencing… CONTINUE READING
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