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Databases to Efficiently Manage Medium Sized, Low Velocity, Multidimensional Data in Tissue Engineering
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VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data

F Musacchia1, A Ciolfi2, M Mutarelli3

  • 1Telethon Institute for Genetics and Medicine, Viale Campi Flegrei, 34, 80078, Pozzuoli (Naples), Italy. f.musacchia@tigem.it.

BMC Bioinformatics
|December 14, 2018
PubMed
Summary

VarGenius is a new software tool that streamlines the analysis of targeted resequencing data for identifying genetic mutations. It efficiently manages multiple samples and analyses, enabling faster and more organized research into Mendelian diseases.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Targeted resequencing is a primary method for identifying genetic mutations in Mendelian diseases.
  • The increasing volume of next-generation sequencing (NGS) data necessitates efficient analysis tools.
  • Existing open-source tools lack integrated capabilities for simultaneous multi-sample analysis and organization.

Purpose of the Study:

  • To develop a versatile command-line software for analyzing multiple targeted resequencing datasets concurrently.
  • To create a centralized database for storing variant data and sample information.
  • To facilitate cohort-based analyses, moving beyond single-sample studies.

Main Methods:

  • VarGenius is a Linux-based command-line software utilizing parallel computing.
  • It integrates the Genome Analysis Tool-Kit (GATK) best practices pipeline for variant calling.
  • Variant annotation is performed using Annovar, with results presented via a web interface.

Main Results:

  • VarGenius enables customizable pipelines for analyzing multiple targeted resequencing data in parallel.
  • It stores analysis outputs (quality statistics, annotations, frequencies) and sample details (genotypes, phenotypes).
  • Demonstrated efficient analysis of whole exome sequencing (WES) and targeted panels, significantly reducing processing time.

Conclusions:

  • VarGenius is a flexible "master" tool addressing the growing demand for heterogeneous NGS analyses.
  • It supports cohort-centered analyses and programmatic data access, enhancing research capabilities.
  • The software is suitable for routine use by biomedical researchers and offers advanced options for computational biologists.