The ATAV command line tool is the interface to ATAV database. Written in java, ATAV consists of three modules. (i) The command line parser and query engine translate user defined parameters and the input sample list (in PLINK’s ped format18) into an efficient SQL query for interrogating the relational database, (ii) A runtime variant object creator parses SQL output into a collection of variant objects. Each variant object includes variant information (genomic coordinates, annotation), variant calls in sample list, sample genotype calls at co-ordinates without a called variant and external annotation data. (iii) A statistical analyses module iterates over the variant objection collection to perform downstream analyses. ATAV currently supports tests for diagnostic analyses such as identifying putative de novo and inherited genotypes of interest in trios, and a framework for performing region-based rare-variant collapsing analyses that identify genes or other genomic units that carry an excess of qualifying variants among cases in comparison to the background variation observed in internal controls of convenience in ATAV database.
The modularized ATAV framework makes it extensible to continuously develop new functions that operate on sequencing/variant data sets. Critical to data integrity, all ATAV analyses allow an auditable log of software and database version, filter parameters adopted, the input sample lists used in the specific run and the runtime logs that ensure full reproducibility.
Source code: https://github.com/nickzren/atav
Any questions, please contact Nick Ren (firstname.lastname@example.org)
If you use ATAV for publication, please cite:
Zhong Ren, Gundula Povysil, David B. Goldstein. (2020) ATAV - a comprehensive platform for population-scale genomic analyses. bioRxiv DOI: "10.1101/2020.06.08.136507":https://doi.org/10.1101/2020.06.08.136507