An Intuitive Workflow to Retrieve Somatic Mutations in Next Generation Sequencing Studies

  • Daniel Glez-Peña
  • Miguel Reboiro-Jato
  • Florentino Fdez-Riverola
  • David G. Pisano
  • Gonzalo Gómez-López
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 93)

Abstract

Next-generation sequencing (NGS) experiments are generating large genome position files (GPFs) to be analyzed in order to report genomic variants of interest (i.e. mutations, indels, etc.). PileLine software implements a novel command-line toolbox for efficient handling, filtering, and comparison of GPFs commonly employed in NGS data analysis workflows (i.e pileup, vcf, bed, and gff). Its functions may be piped with standard UNIX commands in a standard PC being designed to be memory efficient by performing on-disk operations over sorted GPFs directly.In this report we introduce a case study to analyze single nucleotide variants in order to retrieve somatic mutations by using PileLine functionalities. The source code of the software can be downloaded at http://sourceforge.net/projects/pilelinetools/

Keywords

next-generation sequencing pileup vcf single nucleotide variants 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Daniel Glez-Peña
    • 1
  • Miguel Reboiro-Jato
    • 1
  • Florentino Fdez-Riverola
    • 1
  • David G. Pisano
    • 2
  • Gonzalo Gómez-López
    • 2
  1. 1.ESEI: Escuela Superior de Ingeniería InformáticaUniversity of Vigo, Edificio PolitécnicoOurenseSpain
  2. 2.Bioinformatics Unit (UBio), Structural Biology and Biocomputing ProgrammeSpanish National Cancer Research Centre (CNIO)MadridSpain

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