The -sortout option for bedtools coverage is present at the manual web page (http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html), however does not show up with bedtools coverage -h.
Most importantly, bedtools coverage performs EXACTLY the same with or without the -sortout option.
When I do:
I get exactly the same outcome (same file size, same number of lines, same values) as without -sortout option. It's clear that -sortout option does not work. Bedtools version 2.26.0.
The -sortout option for bedtools coverage is present at the manual web page (http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html), however does not show up with bedtools coverage -h. Most importantly, bedtools coverage performs EXACTLY the same with or without the -sortout option. When I do:
bedtools coverage -sortout -a windows.bed \ -b file1.bed file2.bed file3.bed > bedtools.coverage.bed
I get exactly the same outcome (same file size, same number of lines, same values) as without -sortout option. It's clear that -sortout option does not work. Bedtools version 2.26.0.