Quick Sequencing Depth and Coverage Check



This tutorial teaches how to run a quick sequencing depth and coverage check for one or more reference sequences.

1. Sequencing Depth and Coverage Check Using Samtools

In bioinformatics, very often checking for the coverage and depth of a given reference sequence is required.

Samtools introduced on version 1.10 a “coverage” as a sub-command which can be used to process BAM files and return the coverage and other useful metrics (listed below) for each of the reference sequences.

The tool usage is pretty simple:

$ samtools coverage BAM_file -o OUTPUT

The call returns the follow columns:

  • 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

For more information on the sub-command and filters, please check the help with “samtools coverage -h”.

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