Extract coverage information from IGV

Question

[K.Gee]

Hello! I'm using IGV to visualize paired ends into a genome. I marked a target area by using the "Define a region of interest " option from the main toolbar. Also I activated the bases coverage. Unfortunately, I didn't find a way to extract this area information (coverage information). Does anyone knows how to manage this? Thanks in advance!

[K.Gee]

Thanks for the prompt response! I did it and works. In the same line, I have another question: When I click in coverage position in IGV I got a pop up window which contains except the total count the number of nucleotides and its percentage. Do you know if it is possible to obtain this info too? I used samtools depth -r (range) file.bam and I get the total count. The rest options of samtools depth doest seems to do what I am looking for.

[Pierre Lindenbaum]

use 'samtools mpileup'

[Pierre Lindenbaum]

see Coverage In Bam File - Bases And Overall Count

[K.Gee]

thanks a lot!!!!!!!

[Pierre Lindenbaum]

please check the green tick on the left to validate+close.

Answer 1

[Pierre Lindenbaum]

use a command-line tool like "samtools depth"