VarGenius

VarGenius is a Linux-based command-line software for targeted resequencing analysis in next-generation sequencing (NGS) laboratories. It enables customizable pipelines for analyzing multiple datasets in parallel and includes a database for storing analysis outputs and sample information. VarGenius performs joint analysis of numerous samples, follows Genome Analysis Tool-Kit (GATK) best practices for variant calling, and uses Annovar for variant annotation. It has been tested on a parallel computing cluster, demonstrating its capacity to handle large datasets efficiently.

Topic

DNA mutation

Detail

  • Operation: -

  • Software interface: Command-line interface

  • Language: R,Perl

  • License: GNU General Public License, version 3

  • Cost: Free with restrictions

  • Version name: 1.0

  • Credit: The Telethon Undiagnosed Disease Program.

  • Input: -

  • Output: -

  • Contact: Musacchia f.musacchia@tigem.it

  • Collection: -

  • Maturity: Stable

Publications

  • VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database.
  • Musacchia F, et al. VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database. VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database. 2018; 19:477. doi: 10.1186/s12859-018-2532-4
  • https://doi.org/10.1186/s12859-018-2532-4
  • PMID: 30541431
  • PMC: PMC6291943

Download and documentation

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