We have developed a bioinformatics tool, TREAT, which addresses the current challenges in analyzing and interpreting targeted and whole exome sequencing data. The annotations provided by TREAT have been carefully evaluated and selected from a pool of available open source tools and databases, and complimented by additional in-house developed annotations (details at the TREAT website). The variant reports in Excel format integrate the visualizations of the sequence alignment at variant positions, pathways and expression specificity of the variant hosting genes via clickable hyperlinks for each reported INDELs and SNVs. In addition, the summary of the targeted resequencing results is stored in a centralized HTML report with links to the TREAT website, the targeted region coverage report and the read QC report, the description of the TREAT workflow, and links to the website of the annotation tools and databases.
For maximum flexibility, two versions of TREAT were implemented: an annotation only version, and a version integrating read alignment, variant calling and annotations. Both versions can be downloaded as local installations or as Amazon Cloud images which makes TREAT available for users with no access to local bioinformatics infrastructures. By targeting all user groups and enabling rapid integration of emerging analytic methods, we believe that TREAT provides a sustainable NGS analytic workflow with wide applicability to the research community.
We plan to continue adding new functionality and features to TREAT to make it a comprehensive tool for targeted and exome analysis. These include the development of an in-house variant database that collects all variants detected from hundreds of individuals with various types of diseases using exome and whole genome sequencing. This database will provide critical annotations whether the observed variants are truly ‘novel’ or disease specific. In addition, we are in the process of making TREAT applicable to whole genome sequencing data analysis, this would require adding annotation tracks for non-coding regions such as the conservations and regulatory domains.
In summary, the rich set of annotations provided by TREAT, the easy to use, centralized HTML summary report, and the Excel-formatted variant reports with hyperlinked visualization utilities enable the filtering of detected variants based on their functional characteristics, and allow the researchers to navigate, filter and elucidate tens of thousands of variants to focus on potential disease-associated variant(s).