bedtools genomecov .genome file usage

Question

[kaston]

I'm using the bedtools genomecov command to find coverage stats for a human genome alignment:

bedtools genomecov -ibam foo.bam

The bedtools documentation 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 haven't 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?

Thanks

Answer 1

[Aaronquinlan]

With a BAM file, this is unnecssary. Sorry for the confusing docs.

Answer 2

[kaston]

thanks for the prompt reply!

[scchess]

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