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


Ontology type: schema:Chapter     


Chapter Info

DATE

2011

AUTHORS

Daniel Glez-Peña , Miguel Reboiro-Jato , Florentino Fdez-Riverola , David G. Pisano , Gonzalo Gómez-López

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/ More... »

PAGES

83-86

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-642-19914-1_12

DOI

http://dx.doi.org/10.1007/978-3-642-19914-1_12

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1044802775


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