Introduction

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.

Publications

  1. PEMapper and PECaller provide a simplified approach to whole-genome sequencing.
    Cite this
    Johnston HR, Chopra P, Wingo TS, Patel V, , Epstein MP, Mulle JG, Warren ST, Zwick ME, Cutler DJ, 2017-03-01 - Proceedings of the National Academy of Sciences of the United States of America

Credits

  1. H Richard Johnston
    Developer

    Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health

  2. Pankaj Chopra
    Developer

    Department of Human Genetics, Emory University School of Medicine, United States of America

  3. Thomas S Wingo
    Developer

    Department of Neurology, Emory University School of Medicine

  4. Viren Patel
    Developer

    Department of Human Genetics, Emory University School of Medicine, United States of America

  5. Michael P Epstein
    Developer

    Department of Human Genetics, Emory University School of Medicine, United States of America

  6. Jennifer G Mulle
    Developer

    Department of Epidemiology, Emory University Rollins School of Public Health

  7. Stephen T Warren
    Developer

    Department of Biochemistry, Emory University School of Medicine

  8. Michael E Zwick
    Developer

    Department of Human Genetics, Emory University School of Medicine, United States of America

  9. David J Cutler
    Investigator

    Department of Human Genetics, Emory University School of Medicine, United States of America

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Summary
AccessionBT003652
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByDavid J Cutler