Hi,
I have read quite a few posts here about coverage already. But I still had a few questions. I have a BAM file I'm trying to find the coverage of it (typically like say 30X).
So, I decided to use
genomeCoverageBed for my analysis. And I used the following command:genomeCoverageBed -ibam file.bam -g ~/refs/human_g1k_v37.fasta > coverage.txt
As many are aware, the output of the file looks something like this:
genome 0 26849578 100286070 0.26773
genome 1 30938928 100286070 0.308507
genome 2 21764479 100286070 0.217024
genome 3 11775917 100286070 0.117423
genome 4 5346208 100286070 0.0533096
genome 5 2135366 100286070 0.0212927
genome 6 785983 100286070 0.00783741
genome 7 281282 100286070 0.0028048
genome 8 106971 100286070 0.00106666
genome 9 47419 100286070 0.000472837
genome 10 27403 100286070 0.000273248
To find the coverage, I multiplied col2 (depth) with col3 (number of bases in genome with that depth) and then summed the entire column. Then, I divided it by genome length to get the coverage. In this case, col2 * col3 is:0
30938928
43528958
35327751
21384832
10676830
4715898
1968974
855768
426771
274030
And the sum is: 150098740. Since the genome length is 1002860 ...