What it does

This tool runs the samtools coverage command.

Computes the depth at each position or region and draws an ASCII-art histogram or tabulated text. If you select to pool the bam files, then it calculates coverage for the combined files.

The tabulated form uses the following headings:

• rname Reference name / chromosome
• startpos Start position
• endpos End position (or sequence length)
• numreads Number reads aligned to the region (after filtering)
• covbases Number of covered bases with depth >= 1
• coverage Proportion of covered bases [0..1]
• meandepth Mean depth of coverage
• meanbaseq Mean baseQ in covered region
• meanmapq Mean mapQ of selected reads