Unable to view BAM files in IGV

Question

[N-may]

I am trying to open a BAM file (data from human tumor) in IGV to look for mutations in a specific region. However I am not able to view anything on the alignment track.

I am fairly new to IGV and am not sure what I am doing wrong

I installed IGV recently (Java included for MacOS). The .bam and .bam.bai files are in the same folder I am trying to load the file from.

I did not change anything in the preferences when I initially tried loading the file and still saw nothing in the alignment track after zooming all the way in !

[Pierre Lindenbaum]

are you just sure there is any read overlapping the interval ?

what is the output of:

samtools view your.bam "chr7:30387445-30387516"

[biofalconch]

It would be great if you told us what you did beforehand. Did you sorted and indexed your bam file?

[N-may]

Hi. Yes the bam file is already sorted and indexed. I replied to my post earlier saying that the problem is solved now (After closing and opening IGV several times and zooming in and out, the reads are finally showing).

I guess the older replies to this post disappeared after the image which was a separate comment was moved by another user to my original post

[Ram]

I've moved things around and the answer should be visible now. Sorry for the confusion!

Answer 1

[N-may]

I realized I focused on the wrong region in the screenshot when you asked what the output is for the particular region in the image. I went back to IGV to focus on the correct region (which I had already done like 80 times before), and lo and behold, I can suddenly see reads and everything else in the alignment track! Thank you

[GenoMax]

You also appear to be using hg19 genome. If that is not the correct genome build then you could be looking at a wrong region. Be sure to choose the correct genome build in drop-down menu.