I'm using the bedtools genomecov command to find coverage stats for a human genome alignment:
bedtools genomecov -ibam foo.bam
The bedtools documentation (http://bedtools.readthedocs.org/en/latest/content/overview.html) says that you need to specify a .genome file so the tool knows how big the chromosomes are using the "-g filename.genome" option. I havenèt done this, but the command still works.
How does it know what the chromosome sizes are? Is it pointing to a .genome file somewhere in the system that I'm not aware of or is this simply not necessary contrary to the documentation?