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

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

Author information

1
Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
2
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA.
3
Departments of Biomedical Engineering and Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA.

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

PMID:
28637275
PMCID:
PMC5570013
DOI:
10.1093/gigascience/gix045
[Indexed for MEDLINE]
Free PMC Article

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