sequence coverage format trouble

[OTU]

Hi everyone!

I am using bowtie2 to map my reads on scaffolds and I would like to know, is there a way to get a coverage calculation in samtools? I know that I can use BEDTools, but how can I get .bed format from bam? And for my analysis pipeline I need .csv format of coverage information, which is not created in BEDTools.
Any ideas how I can do this?


Help!:

[GenoMax]

There are several solutions on this biostars page including a "samtools depth" one: http://www.biostars.org/p/5165/

[OTU]

Thank you!
However, I wasn't able to find a way to get the information on coverage to be in csv format.
I used this:
samtools depth *bamfile* | awk '{sum+=$3} END { print "Average = ",sum/NR}'

And got the number. Is there a way to get it in csv format?

[dpryan]

samtools depth *bamfile* | awk '{sum+=$3} END { printf("Average,%f\n",sum/NR)}' > some_file.csv

Will make the output comma separated (csv is just a text file with commas as column separators).

[GenoMax]

That awk script only prints a single number for the whole bam so that is probably not the output OTU is looking for.

@OTU Are you looking to get a "depth" number for each scaffold?