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Bioinformatics. 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.

Author information

1
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo College of Medicine, Rochester, MN, USA.

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.

PMID:
22088845
PMCID:
PMC3259432
DOI:
10.1093/bioinformatics/btr612
[Indexed for MEDLINE]
Free PMC Article
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