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. 2012 Jan 15;28(2):277-8.
doi: 10.1093/bioinformatics/btr612. Epub 2011 Nov 15.

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Yan W Asmann  1 , Sumit Middha, Asif Hossain, Saurabh Baheti, Ying Li, High-Seng Chai, Zhifu Sun, Patrick H Duffy, Ahmed A Hadad, Asha Nair, Xiaoyu Liu, Yuji Zhang, Eric W Klee, Krishna R Kalari, Jean-Pierre A Kocher
Affiliations

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Yan W Asmann et al. Bioinformatics. .

Abstract

TREAT (Targeted RE-sequencing Annotation Tool) is a tool for facile navigation and mining of the variants from both targeted resequencing and whole exome sequencing. It provides a rich integration of publicly available as well as in-house developed annotations and visualizations for variants, variant-hosting genes and host-gene pathways.

Availability and implementation: TREAT is freely available to non-commercial users as either a stand-alone annotation and visualization tool, or as a comprehensive workflow integrating sequencing alignment and variant calling. The executables, instructions and the Amazon Cloud Images of TREAT can be downloaded at the website: http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.

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