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/
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Glez-Peña, D., Reboiro-Jato, M., Fdez-Riverola, F., Pisano, D.G., Gómez-López, G. (2011). An Intuitive Workflow to Retrieve Somatic Mutations in Next Generation Sequencing Studies. In: Rocha, M.P., Rodríguez, J.M.C., Fdez-Riverola, F., Valencia, A. (eds) 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Advances in Intelligent and Soft Computing, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19914-1_12
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DOI: https://doi.org/10.1007/978-3-642-19914-1_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-19913-4
Online ISBN: 978-3-642-19914-1
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