Integrated tools assist researchers with identifying variants of
interest in next-generation sequencing (NGS) data
Building on and extending leading tools for annotating, filtering, and visualizing mutations in genetic data, the VAA Suite helps researchers rapidly pinpoint those variants associated with specific diseases, including cancer and inherited diseases with known genetic causes. The Suite adds descriptive annotations to the large, text-based variant call format (VCF) files generated by NGS analysis software. It also provides advanced filtering and visualization options that enable researchers to sort through data to find those variants most relevant to their studies.
“The challenge in NGS analysis is reliably identifying the variants in an individual genome that may be associated with disease,” said Trevor Heritage, vice president of corporate development and strategy at Appistry. “The VAA Suite enables researchers to benefit from the collected wisdom of their colleagues to focus on those mutations worthy of closer examination.”
Appistry’s VAA Suite includes VarSeeker, an Appistry-enhanced version of the VarSifter open-source program for reading VCF files and displaying them for inspection and analysis. VarSeeker provides generic filtering capabilities that enable researchers to sort on all of the data in a VCF file. It also includes a graphical user interface that makes it easier to researchers to sort, query, visualize, and save data.
Appistry has constructed a set of methods for downloading and converting datasources for use by tools in the VAA Suite. A set of starter datasources come as part of the Suite. Rounding out the VAA Suite are tools for annotating VCF files based on the datasources and filtering and manipulating annotated files. Appistry has also developed a series of scripts that automatically perform annotations and common filtering steps, such as sorting variants according to population frequency or deleteriousness.
While specifically designed for use with Appistry’s Genome Analysis Toolkit (GATK) and Cancer Genome Analysis (CGA) Suite, the VAA Suite works with any tools that generate VCF files.
Appistry will be delivering a webinar introducing the VAA Suite