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

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.). Pile Line 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 Pile Line functionalities. The source code of the software can be downloaded at http://sourceforge.net/projects/pilelinetools/