Samtools coverage vs samtools depth for % coverage
I want to calculate the % coverage of my assembly based on reference mapping. Should I use samtools coverage or samtools depth?
• 3,734 views
•
link
1 answer
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
http://www.htslib.org/doc/samtools-coverage.html
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.
• 0 views
•
link
Log in to answer this question.