Tool(s) for calculating depth and genome coverage

[cheezemeister]

I am looking for a tool that can take my BAM files and spit out the following information:

1. Mean depth across the entire genome
2. Percent of genome covered at a specified depth, or preferably multiple specified depths (i.e. 10X, 20X, 30X etc).

I'm not a great command line jockey, so a tool that can be installed in Galaxy would be great, but if not, then I can muddle my way through it on the command line.

Thanks!

[GenoMax]

http://seqanswers.com/forums/showthread.php?t=17253

[cheezemeister]

I've got Bedtools Genome Coverage working in Galaxy now, but the output is confusing. It seems to pick randomly-sized intervals and report a coverage value across that interval. Example output below:

chr 3 6 2
chr 6 13 3
chr 13 14 5
chr 14 16 6
chr 16 25 8
chr 25 27 10
chr 27 29 12
chr 29 32 15
chr 32 47 16
chr 47 60 18
chr 60 72 19
chr 72 84 21

Really, all I want is a single number: mean depth across the entire genome. Is there a simple way to get this number using this tool?

[GenoMax]

There are multiple solutions here but you will need to leave the confines of galaxy and work on the command line: https://www.biostars.org/p/5165/

[Brian Bushnell]

You can calculate it yourself quite easily, if you have fixed-length reads - (#mapped reads)*(read length)/(genome size).

[cheezemeister]

You can calculate it yourself quite easily, if you have fixed-length reads - (#mapped reads)*(read length)/(genome size).

Not fixed length, unfortunately. They've been adapter and quality trimmed, although your method would still give me an estimate.

I actually found from reading another thread on here that the easiest way for me was to just load the BAMs into Qualimap and look at the summary page, as Qualimap calculates that value as part of its analysis.

[cheezemeister]

There are multiple solutions here but you will need to leave the confines of galaxy and work on the command line: https://www.biostars.org/p/5165/

I found this same thread on Biostars. I was going to try out some of the suggestions there when I read the very last entry about Qualimap. Since I needed these numbers fairly quickly, I just used that, but I'm going to try out come of the command line options for future use, because Qualimap does do batches very well.

[shimbalama]

GATK DepthOfCoverage is command line but very easy to use and well documented on their site. Beyond that I normally use custom scripts based on a pile up. All of these options will require a lot of RAM for a whole genome, so if you can use an interval list/bed file that'll makes things much easier/faster.

[shashibioinfo]

Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only chr2

Hey for a specific chromosome number how to do coverage analysis for input bam file using bedtools and GATK tools

Thanks