PileLine

PileLine manages, filters, compares, and annotates genomic position (GP) files produced by next-generation sequencing (NGS) to enable analysis of covered genomic positions and support somatic mutation finding studies.

Key Features:

• Command-line toolkit: Handles, filters, compares, and annotates genomic position (GP) files that represent each covered genomic position with at least one aligned read from NGS experiments.
• File format support: Supports Variant Call Format (VCF), SAMTools pileup, BED, and GFF file formats.
• Memory-efficient on-disk processing: Achieves memory efficiency through fast on-disk operations over sorted GP files.
• Genome browser module (PileLineGUI): Includes a genome browser module to inspect GP files and support somatic mutation finding studies.
• Implementation and platform compatibility: Implemented in Java and compatible with UNIX (Linux, Mac OS) and Windows platforms.
• Performance: Tools have undergone extensive testing to ensure high performance.
• License: Distributed under the GNU LGPL license.

Scientific Applications:

• Somatic mutation finding: Inspection of GP files with the genome browser module to support somatic mutation finding studies.
• GP-level analysis and annotation: Management, filtering, comparison, and annotation of GP files from NGS experiments for genomic analyses.

Methodology:

Operates on sorted genomic position (GP) files using fast on-disk operations to reduce memory usage; implemented in Java and tested for high performance.