covtobed

covtobed converts coverage information from sorted BAM files into BED format to represent per-position sequencing depth for downstream analysis and visualization.

Key Features:

• Coverage Extraction: Extracts depth of coverage at each genomic position from sorted BAM files.
• Customizable Output: Allows specification of a genomic range of interest and a minimum feature length threshold for inclusion in the BED output.
• BAM Parsing: Parses BAM files using libbamtools.
• Implementation: Implemented in C++.
• Streamlined I/O: Supports input and output streams consistent with a single-purpose Unix-style design.

Scientific Applications:

• Variant calling support: Provides per-position coverage information to inform variant-calling workflows.
• Coverage profiling: Identifies genomic regions with low or high sequencing depth for quality control and analysis.
• Visualization preparation: Produces BED-format intervals suitable for visualization tools that accept BED input.

Methodology:

Parses sorted BAM files with libbamtools, computes per-position depth, applies user-specified range and minimum-length filters, and emits BED intervals; implemented in C++ with stream I/O support.