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 !
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N-may •
1 answer
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
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are you just sure there is any read overlapping the interval ?
what is the output of:
It would be great if you told us what you did beforehand. Did you sorted and indexed your bam file?
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
I've moved things around and the answer should be visible now. Sorry for the confusion!