HPexome: An automated tool for processing whole-exome sequencing data

Author(s)

Cendes, Lucas L. ^{[1, 2, 3]} ; de Souza, Welliton ^{[1, 4]} ; Lopes-Cendes, Iscia ^{[1, 4]} ; Carvalho, Benilton S. ^{[5, 1]}

Affiliation

^[1] Univ Campinas UNICAMP, Brazilian Inst Neurosci & Neurotechnol BRAINN, Campinas, SP - Brazil

^[2] Amer Sch Campinas, Campinas, SP - Brazil

^[3] Univ Washington, Paul G Allen Sch Comp Sci & Engn, Seattle, WA 98195 - USA

^[4] Univ Campinas UNICAMP, Sch Med Sci, Dept Med Genet & Genom Med, Campinas, SP - Brazil

^[5] Univ Campinas UNICAMP, Inst Math Stat & Sci Comp, Dept Stat, Campinas, SP - Brazil

• Document type: Journal article
• Source: SOFTWAREX; v. 11, JAN-JUN 2020.
• Web of Science Citations: 0

Abstract

Whole-exome sequencing has been widely used in clinical applications for the identification of the genetic causes of several diseases. HPexome is a command-line tool that automates many data processing tasks for exome-sequencing data analysis of large-scale cohorts. Given ready-analysis alignment files, HPexome breaks input data into smaller pieces defined by genomic regions and efficiently processes them in parallel using cluster-computing environments. It relies on the Queue workflow execution engine, GATK variant calling tool, and its best practices to output a high-confident multi-sample genomics variant file. (c) 2020 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). (AU)

• FAPESP's process: 13/07559-3 - BRAINN - The Brazilian Institute of Neuroscience and Neurotechnology
• Grantee: Fernando Cendes
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 16/04204-8 - Development and optimization of bioinformatics protocols and tools through high-performance computing techniques for use in processing large scale biological data
• Grantee: Wélliton de Souza
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 12/21548-1 - Multimodal investigation of epileptogenesis with emphasis in the implementation of new animal models and new tools
• Grantee: Benilton de Sá Carvalho
• Support Opportunities: Scholarships in Brazil - Post-Doctoral