16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
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Abstract
Summary
16GT is a variant caller for Illumina WGS and WES germline data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT ran faster and demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy in calling indels as compared to the GATK HaplotypeCaller.
Availability and implementation
https://github.com/aquaskyline/16GT
Contact
rluo5@jhu.edu
Supplementary information
Supplementary tables and notes are available at Bioinformatics online.
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Now published in GigaScience doi: 10.1093/gigascience/gix045
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix045 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100738 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100737
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