mosdepth

mosdepth calculates genome-wide sequencing coverage by processing BAM and CRAM files to measure per-nucleotide depth across whole-genome, exome, and targeted sequencing regions.

Key Features:

• Computational efficiency: Uses a simple, computationally efficient algorithm to produce coverage summaries rapidly.
• Input formats: Processes BAM and CRAM files to derive coverage information.
• Per-nucleotide and region-level depth: Calculates sequencing depth at each nucleotide position and within specified genomic regions.
• Region specification: Accepts BED files for capture-region evaluation and supports fixed-size windows useful for copy-number calling.
• Output options: Generates coverage summaries and various coverage profiles for downstream analyses.

Scientific Applications:

• Whole-Genome Sequencing (WGS): Calculates per-nucleotide depth across the genome to support comprehensive WGS coverage analyses.
• Exome and Targeted Sequencing: Evaluates coverage across capture regions to assess sequencing efficiency and depth uniformity in exome and targeted experiments.
• Copy-Number Analysis: Uses fixed-size window coverage summaries to facilitate copy-number calling by comparing coverage across windows.

Methodology:

Reads BAM or CRAM files and calculates sequencing depth at specified positions or regions (including BED regions or fixed-size windows) using a computationally efficient algorithm to produce coverage summaries.