VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database
Autor: | Musacchia, F., Ciolfi, A., Mutarelli, M., Bruselles, A., Castello, R., Pinelli, M., Basu, S., Banfi, S., Casari, G., Tartaglia, M., Nigro, V., Torella, Annalaura, ESPOSITO, GAIA, Cappuccio, Gerarda, Mancano, Giorgia, Maitz, Silvia, Brunetti-Pierri, Nicola, Parenti, Giancarlo, Selicorni, Angelo |
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Přispěvatelé: | Musacchia, F., Ciolfi, A., Mutarelli, M., Bruselles, A., Castello, R., Pinelli, M., Basu, S., Banfi, S., Casari, G., Tartaglia, M., Nigro, V., Torella, Annalaura, Esposito, Gaia, Cappuccio, Gerarda, Mancano, Giorgia, Maitz, Silvia, Brunetti-Pierri, Nicola, Parenti, Giancarlo, Selicorni, Angelo, Torella, A., Esposito, G., Cappuccio, G., Mancano, G., Maitz, S., Brunetti-Pierri, N., Parenti, G., Selicorni, A. |
Jazyk: | angličtina |
Rok vydání: | 2018 |
Předmět: |
0301 basic medicine
Databases Factual Cost effectiveness computer.software_genre lcsh:Computer applications to medicine. Medical informatics Genome Biochemistry 03 medical and health sciences Annotation chemistry.chemical_compound 0302 clinical medicine Structural Biology Computer cluster Humans Allele lcsh:QH301-705.5 Molecular Biology Exome sequencing Database Applied Mathematics Computational Biology High-Throughput Nucleotide Sequencing Computer Science Applications1707 Computer Vision and Pattern Recognition Sequence Analysis DNA Pipeline (software) Computer Science Applications 030104 developmental biology chemistry lcsh:Biology (General) lcsh:R858-859.7 Line (text file) DNA microarray computer 030217 neurology & neurosurgery DNA Software Human |
Zdroj: | BMC Bioinformatics, Vol 19, Iss 1, Pp 1-14 (2018) BMC Bioinformatics |
Popis: | Background Targeted resequencing has become the most used and cost-effective approach for identifying causative mutations of Mendelian diseases both for diagnostics and research purposes. Due to very rapid technological progress, NGS laboratories are expanding their capabilities to address the increasing number of analyses. Several open source tools are available to build a generic variant calling pipeline, but a tool able to simultaneously execute multiple analyses, organize, and categorize the samples is still missing. Results Here we describe VarGenius, a Linux based command line software able to execute customizable pipelines for the analysis of multiple targeted resequencing data using parallel computing. VarGenius provides a database to store the output of the analysis (calling quality statistics, variant annotations, internal allelic variant frequencies) and sample information (personal data, genotypes, phenotypes). VarGenius can also perform the “joint analysis” of hundreds of samples with a single command, drastically reducing the time for the configuration and execution of the analysis. VarGenius executes the standard pipeline of the Genome Analysis Tool-Kit (GATK) best practices (GBP) for germinal variant calling, annotates the variants using Annovar, and generates a user-friendly output displaying the results through a web page. VarGenius has been tested on a parallel computing cluster with 52 machines with 120GB of RAM each. Under this configuration, a 50 M whole exome sequencing (WES) analysis for a family was executed in about 7 h (trio or quartet); a joint analysis of 30 WES in about 24 h and the parallel analysis of 34 single samples from a 1 M panel in about 2 h. Conclusions We developed VarGenius, a “master” tool that faces the increasing demand of heterogeneous NGS analyses and allows maximum flexibility for downstream analyses. It paves the way to a different kind of analysis, centered on cohorts rather than on singleton. Patient and variant information are stored into the database and any output file can be accessed programmatically. VarGenius can be used for routine analyses by biomedical researchers with basic Linux skills providing additional flexibility for computational biologists to develop their own algorithms for the comparison and analysis of data. The software is freely available at: https://github.com/frankMusacchia/VarGenius Electronic supplementary material The online version of this article (10.1186/s12859-018-2532-4) contains supplementary material, which is available to authorized users. |
Databáze: | OpenAIRE |
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