bedtools genomecov .genome file usage
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6.2 years ago
kaston ▴ 40

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?

Thanks.

 

bedtools genomecov • 5.3k views
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6.2 years ago

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

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6.2 years ago
kaston ▴ 40

thanks for the prompt reply!

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