I'm currently working on some scRNAseq data and looked for reads in my BAM file that mapped over a known mutation we found in that sample. So first I used bamtools intersect to check if there are any reads that overlap the mutation and found that there should be a few in JAK2. Then I wanted to inspect them visually in a genome browser and used IGV because that's what I've used so far. Interestingly, no reads overlap the position of interest. When I load the same BAM file into IGB however I see what I expected.
I made sure to select hg19 in both cases.
Does anybody have an idea what's going on here?
I attached screenshots so you get an idea of what I'm talking about.