I want to calculate the % coverage of my assembly based on reference mapping. Should I use samtools coverage or samtools depth?
Coverage and depth are not identical concepts, though are related.
samtools depth will give you the depth at each coordinate,
samtools coverage can directly report other characteristics as well: for example what percent of bases are covered
samtools coverage can be thought of as a convenience utility added later, well after samtools depth. You can compute everything that samtools coverage reports from samtools depth output with a custom data analysis process.
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy