igv and bam file

Question

[biology_inform]

Hi all,

I have a quick and probably easy question. I am new to igv and I want to find the number of alignments in the bam file which aligned to genome. (To be clear I am trying to find number of alignments in the red box which indicated in the image)

Thanks in advance :)

[swbarnes2]

Have you tried bedtools?

[biology_inform]

nope i didnt. Which function should I use?