Genomics Research Tools

Genome Analysis Toolkit


Next-generation sequencing analysis demands high-quality, accurate results and the flexibility to tackle a range of analysis problems. The Genome Analysis Toolkit (GATK) was built to provide actionable results from modern NGS datasets.

The GATK from Appistry enables researchers to

  • Process data from any NGS platform
  • Choose from over 70 tools to tackle the entire NGS analysis workflow
  • Handle any type of genetic data—exomes or whole genomes, human or non-human DNA, and even RNA
  • Undertake complex analyses, including trio analysis, RNA sequencing, biomarker discovery, and clinical trial stratification
  • Get up and running fast with guided workflows that include configuration scripts, test datasets, and results summaries
  • Implement pipelines quickly and consistently through controlled releases and user-centered support


Key Features

Diagnostics and quality control

Several GATK tools clean and standardize BAM files to ensure accuracy and streamline variant analysis

Sequence data processing

The GATK’s Base Quality Score Recalibration, which standardizes the data produced by different sequencers, was highlighted as one of the most important methodologies developed by the 1000 Genomes Pilot Project. The GATK also provides gold-standard tools for realignment.

Variant calling

The GATK’s two variant callers, the Unified Genotyper and the Haplotype Caller, together provide superior sensitivity and specificity whether calling SNPs or Indels.

Variant recalibration, evaluation, and manipulation

Smart filters in the GATK can be used to improve specificity, and other GATK tools help researchers determine which variants are most relevant to an analysis.

Extended Pipelines

Appistry leverages tools from the Broad Institute and other sources to create integrated, end-to-end pipelines for high-value analyses, such as determining variants and differentially expressed genes, pathways, and functions from RNA-Seq data.

GATK Best Practices Workflow for DNA-Seq

Appistry’s Integrated Workflow for RNA-Seq Analysis


Appistry Value

The GATK from Appistry contains the same tools, functionality, and framework found in the academic versions available from the Broad. Appistry makes the GATK easier to use, however, by providing

  • Guided workflows for common analysis tasks, validated on test datasets so that you can calibrate your processes to achieve accurate, high-quality results.
  • Controlled, consistent release schedules. We package all of the Broad’s GATK updates, enhancements, and issue resolutions into managed releases that are easy for busy development teams to implement, particularly in regulated settings. 
  • Interim beta releases offering access to the very latest Broad updates. These releases are not fully QAd and may be less stable than managed updates.
  • Extensive, user-centered help with implementing and deploying the tools, including comprehensive best practices guides, FAQs, technical documentation, and access to on-site support experts at the Broad who will work with you to personally answer your questions. 

What's New?

Appistry released GATK 2014.4 on November 18, 2014. The release is based on Broad version 3.3-0.

Release Notes

  • Analyze non-diploid genomes. The Haplotype Caller is now ploidy capable, making the GATK even better at analyzing plant and microbial samples (and removing any lingering need for the Unified Genotyper, which before was the GATK’s ploidy-capable caller).
  • Flag phased genotypes. Many downstream genetic analyses require accurate genotypes and phasing information. The Haplotype Caller now adds this information directly to the VCF file so that you can rapidly comb through a file to determine which SNPs have been phased together.
  • Call variants more accurately. The Haplotype Caller now does a better job of retaining information at the edges of reads resulting in more sensitive variant calls.

Appistry also released on August 29, 2014 an integrated workflow for analyzing RNA-Seq data. The workflow builds on the GATK Best Practices for calling RNA-Seq variants to include Appistry-built workflows for determining differential expression and pathway/function enrichment. Learn more about this workflow by viewing our webinar.


Any entity using the GATK in any for-profit context or to generate revenue must purchase a license from Appistry. This includes all commercial entities regardless of the nature of the work and any academic or non-profit entity charging a fee for a service that employs the GATK.

Single User and Workgroup Licenses

Academic research teams or small, start-up companies (fewer than 10 employees).

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Small Business Licenses

Provides organizations of less than 50 employees with unlimited access to the GATK.

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Lab, Developer, and Runtime Licenses

Research teams in organizations of greater than 50 employees who need to provide varying levels of access to the GATK.

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Site and Enterprise Licenses

Scaled by organizational size and providing unlimited usage for a single geographical site or unlimited usage across all of an organization’s departments, labs, or geographies.

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