Overview

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.

Getting More from Broad NGS Analysis Tools with Appistry Support

Watch as Craig DeLoughery, customer support director, discusses the importance of one-on-one support in helping labs implement and use Appistry's NGS analysis tools. Length: 1:38

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

The GATK includes several tools for cleaning and standardizing BAM files to ensure accuracy and streamline variant analysis

Sequence data processing

BQSR, called one of the most important methodologies developed by the 1000 Genomes Pilot Project, standardizes the data produced by different sequencers.

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.

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 In Version 2014.4

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

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.