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

  1. Ruibang Luo
  2. Michael C. Schatz
  3. Steven L. Salzberg
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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

<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/aquaskyline/16GT">https://github.com/aquaskyline/16GT</ext-link>

Contact

<email>rluo5@jhu.edu</email>

Supplementary information

Supplementary tables and notes are available atBioinformaticsonline.

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