EXtrACtor, a tool for multiple queries and data extractions from the EXAC and gnomAD database

Abstract

IntroductionEXtrACtor provides an easy and flexible way to perform multiple queries of the ExAC and gnomAD databases (Lek M, al. e, 2016) and process the results. The ExAC browser is an often-used tool to gather information from a large number of exomes while the gnomAD database expands on this by increasing the number of exomes but also adding genomes. However the websites only allow the users to query a single gene, transcript or location at a time. On the other hand downloading the entire database results in other challenges for the average user, especially with the download size for the gnomAD database approaching 100GB. EXtrACtor allows the user to supply a list of genes, transcripts or regions to be queried against either the ExAC or the gnomAD database. At the same time it gives the user a flexible user interface in order to quickly filter on various properties such as cohort, variant type and more.\n\nAvailability and implementationEXtrACtor source code is freely available from https://github.com/dagrim1/extractor and is written in platform independent software Java for use on windows, UNIX and mac.\n\nContactf.mulder@umcutrecht.nl