Treat: A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Yan W. Asmann, 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

Research output: Contribution to journalArticle

45 Scopus citations

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.

Original languageEnglish (US)
Article numberbtr612
Pages (from-to)277-278
Number of pages2
JournalBioinformatics
Volume28
Issue number2
DOIs
StatePublished - Jan 1 2012

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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