title: PEMapper and PECaller provide a simplified approach to whole-genome sequencing.
abstract: The analysis of human whole-genome sequencing data presents significant computational challenges. The sheer size of datasets places an enormous burden on computational, disk array, and network resources. Here, we present an integrated computational package, PEMapper/PECaller, that was designed specifically to minimize the burden on networks and disk arrays, create output files that are minimal in size, and run in a highly computationally efficient way, with the single goal of enabling whole-genome sequencing at scale. In addition to improved computational efficiency, we implement a statistical framework that allows for a base by base error model, allowing this package to perform as well or better than the widely used Genome Analysis Toolkit (GATK) in all key measures of performance on human whole-genome sequences.
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.|Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA 30322.
authors.forename: H Richard
authors.initials: HR
authors.lastname: Johnston
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Chopra
authors.affiliation: Division of Neurology, Atlanta Veterans Affairs Medical Center, Atlanta, GA 30322.|Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.|Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Wingo
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.
authors.forename: Viren
authors.initials: V
authors.lastname: Patel
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Epstein
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.|Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322.
authors.forename: Jennifer G
authors.initials: JG
authors.lastname: Mulle
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322; swarren@emory.edu mzwick@emory.edu djcutle@emory.edu.|Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322.|Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322.
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Warren
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322; swarren@emory.edu mzwick@emory.edu djcutle@emory.edu.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Zwick
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322; swarren@emory.edu mzwick@emory.edu djcutle@emory.edu.
authors.forename: David J
authors.initials: DJ
authors.lastname: Cutler
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software; D000073336:Whole Genome Sequencing / Q000379:methods*
keywords: GATK; SNP calling; genome sequencing; sequence mapping; software