TY - JOUR T1 - BasePlayer: Versatile Analysis Software for Large-scale Genomic Variant Discovery JF - bioRxiv DO - 10.1101/126482 SP - 126482 AU - Riku Katainen AU - Iikki Donner AU - Tatiana Cajuso AU - Eevi Kaasinen AU - Kimmo Palin AU - Veli Mäkinen AU - Lauri A. Aaltonen AU - Esa Pitkänen Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/04/11/126482.abstract N2 - Next-generation sequencing (NGS) is being routinely applied in life sciences and clinical practice, where the interpretation of the resulting massive data has become a critical challenge. Computational workflows, such as the Broad GATK, have been established to take raw sequencing data and produce processed data for downstream analyses. Consequently, results of these computationally demanding workflows, consisting of e.g. sequence alignment and variant calling, are increasingly being provided for customers by sequencing and bioinformatics facilities. However, downstream variant analysis, whole-genome level in particular, has been lacking a multi-purpose tool, which could take advantage of rapidly growing genomic information and integrate genetic variant, sequence, genomic annotation and regulatory (e.g. ENCODE) data interactively and in a visual fashion. Here we introduce a highly efficient and user-friendly software, BasePlayer (http://baseplayer.fi), for biological discovery in large-scale NGS data. BasePlayer enables tightly integrated comparative variant analysis and visualization of thousands of NGS data samples and millions of variants, with numerous applications in disease, regulatory and population genomics. Although BasePlayer has been designed primarily for whole-genome and exome sequencing data, it is well-suited to various study settings, diseases and organisms by supporting standard and upcoming file formats. BasePlayer transforms an ordinary desktop computer into a large-scale genomic research platform, enabling also a non-technical user to perform complex comparative variant analyses, population frequency filtering and genome level annotations under intuitive, scalable and highly-responsive user interface to facilitate everyday genetic research as well as the search of novel discoveries. ER -