Problem with viewing BAM files in IGV
I’m quite new to bioinformatics and I’m having some beginner problems with IGV. I’ve got some BAM files that were generated using the GATK best practice pipeline for SNP discovery, with BAI files located in the same directory. I’m using the latest version of IGV on a Ubuntu 18.04.4 server with Java 11.
Until recently I could open my files without problems, but if I try to open them now, no data are displayed. Below I’ve zoomed in on a region where I know that there should be data (as verified by inspecting the BAM file with samtools view), zooming in further doesn’t help. If I open a saved past session, the data are displayed with all the usual tracks, but I can’t open the data which I used for this saved past session.
Any suggestions on how I can solve / troubleshoot this problem? Thanks!
EDIT: The solution was to select both the BAM and the BAI and to open them simultaneously.
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