16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

Gigascience. 2017 Jul 1;6(7):1-4. doi: 10.1093/gigascience/gix045.

Abstract

16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify single nucleotide polymorphism and insertion and deletion calling in a single variant calling algorithm. In benchmark comparisons with 5 other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling single nucleotide polymorphisms, and it provided comparable sensitivity and accuracy for calling insertions and deletions as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT.

Keywords: Bayesian model; SNP calling; indel calling; variant calling.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Genome-Wide Association Study / methods*
  • Genome-Wide Association Study / standards
  • Genotype*
  • Haplotypes
  • Humans
  • Models, Genetic
  • Polymorphism, Single Nucleotide
  • Probability
  • Sensitivity and Specificity
  • Software*
  • Whole Exome Sequencing / methods*
  • Whole Exome Sequencing / standards