gatk_depth_of_coverage

gatk_depth_of_coverage computes coverage metrics from aligned sequencing reads in BAM files to quantify depth of coverage across loci, intervals, genes, or whole genomes.

Key Features:

• Multi-level analysis: Reports coverage at per-locus, interval, gene, and total (whole-genome) levels.
• Partitioning: Allows partitioning of coverage by sample, read group, sequencing technology, center, or library.
• Statistical summarization: Produces summary statistics including mean, median, quartiles, and percentage of bases covered above specified thresholds.
• Quality filtering: Supports filtering of reads and bases based on mapping quality and base quality scores.
• File and toolkit compatibility: Processes BAM (binary SAM) input and operates within the Genome Analysis Toolkit (GATK) framework.

Scientific Applications:

• Sequencing quality assessment: Evaluates sequencing experiment quality by quantifying depth and coverage uniformity.
• Coverage gap identification: Identifies genomic regions with insufficient or zero coverage for downstream analysis or resequencing decisions.
• Study design and comparison: Facilitates optimization of experimental design and comparison across samples, read groups, technologies, centers, or libraries in large-scale studies.

Methodology:

Processes BAM files (binary Sequence Alignment/Map) using GATK by parsing aligned reads to count per-base coverage and compute coverage metrics across specified genomic regions.