title: TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
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.
  
  
  METHODS
  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.
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo College of Medicine, Rochester, MN, USA.
authors.forename: Yan W
authors.initials: YW
authors.lastname: Asmann
authors.forename: Sumit
authors.initials: S
authors.lastname: Middha
authors.forename: Asif
authors.initials: A
authors.lastname: Hossain
authors.forename: Saurabh
authors.initials: S
authors.lastname: Baheti
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.forename: High-Seng
authors.initials: HS
authors.lastname: Chai
authors.forename: Zhifu
authors.initials: Z
authors.lastname: Sun
authors.forename: Patrick H
authors.initials: PH
authors.lastname: Duffy
authors.forename: Ahmed A
authors.initials: AA
authors.lastname: Hadad
authors.forename: Asha
authors.initials: A
authors.lastname: Nair
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Liu
authors.forename: Yuji
authors.initials: Y
authors.lastname: Zhang
authors.forename: Eric W
authors.initials: EW
authors.lastname: Klee
authors.forename: Krishna R
authors.initials: KR
authors.lastname: Kalari
authors.forename: Jean-Pierre A
authors.initials: JP
authors.lastname: Kocher
mesh_terms: D019295:Computational Biology / Q000379:methods*; D059472:Exome; D006801:Humans; D058977:Molecular Sequence Annotation; D016415:Sequence Alignment; D012984:Software
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