How to compute percentage of my genome covering human reference genome?

[bioinf newbie]

I have the alignment file for my genome (bam).
I want to find out % of genome that covered reference human genome with atleast 1 read, 2 reads, 3 reads, and 4 reads.
How do I go about it?

[svl]

Maybe this can help you:

http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage_v3.0

Requires some work to get it working properly and also I think the documentation is not that clear about what it calculates precisely, but when using the option "-geneList" it outputs what you want (% covered by 1/2/3/50/100/etc)

[colindaven]

Have a look at the samtools depth command too if you struggle with GATK.