Samtools Depth

[Jeromek]

Hey Guys,

I have just installed samtools on the command line and am messing around with the features. One thing I am curious about is deletion detection. Specifically, I am looking to use the depth function with position arguments to check coverage at a specific point. The function however seems to return a list of all locations and their associated depth. Is what I am looking for possible, or do you have to digest the entire data first?

Also, if anyone has good documentation I would appreciate that, as I could not locate any with a quick search. Kind regards, J

[Cytosine]

Samtools does have a really great, almost instant, access to any region of the .bam file because of it's .bai index file.

If you want to extract coverage at a specific point in your genome, then take a look at the samtools depth usage information.

Usage: samtools depth [options] in1.bam [in2.bam [...]]
Options:
   -b <bed>            list of positions or regions
   -f <list>           list of input BAM filenames, one per line [null]
   -l <int>            minQLen
   -q <int>            base quality threshold
   -Q <int>            mapping quality threshold
   -r <chr:from-to>    region

The -r option is the one with which you get coverage report of a specific region.

For example:

samtools depth -r chr1:10000-20000 mymapping.bam

Will extract the coverage information between 10000-20000 bp for the >chr1 entry from mymapping.bam file.

Check out samtools' webpage for more info:
http://samtools.sourceforge.net/

[Jeromek]

Thanks very much! Really Useful