Summary We present ATAV, an analysis platform for large-scale whole-exome and whole-genome sequencing projects. ATAV stores variant and coverage data for all samples in a centralized database, which is then efficiently queried by ATAV to support diagnostic analyses for trios and singletons, as well as rare-variant collapsing analyses for finding disease associations in complex diseases. Runtime logs ensure full reproducibility and the modularized ATAV framework makes it extensible to continuous development of new functions. In recent years ATAV has not only been helpful for identifying disease-causing variants for a range of diseases, but has also enabled the discovery of novel genes by rare-variant collapsing on datasets containing more than 20,000 samples. Analyses to date have been performed on more than 110,000 sequenced individuals demonstrating that the framework is robust to large-scale studies.
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