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

Ruibang Luo, Michael C. Schatz, Steven L. Salzberg

Research output: Research - peer-reviewComment/debate

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.

LanguageEnglish (US)
Article numbergix045
JournalGigaScience
Volume6
Issue number7
DOIs
StatePublished - Jul 1 2017

Fingerprint

Statistical Models
Single Nucleotide Polymorphism
Genotype
Nucleotides
Polymorphism
Exome
Benchmarking
Genome
Servers
Genes

Keywords

  • Bayesian model
  • Indel calling
  • SNP calling
  • Variant calling

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

16GT : A fast and sensitive variant caller using a 16-genotype probabilistic model. / Luo, Ruibang; Schatz, Michael C.; Salzberg, Steven L.

In: GigaScience, Vol. 6, No. 7, gix045, 01.07.2017.

Research output: Research - peer-reviewComment/debate

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