cannot open bam file

[Bmh789 789]

Hi

I am having the same problem as one of the earlier commentators: 

" I am having problems with viewing .BAM files in IGV.

The genome of my interest is loaded and I want to see RNA-seq data.

.bam and .bam.bai files are in the same folder, but when I try loading the .bam file to view the reads, I get the following error massages:

"Error loading SAM header: Cannot use index file with textual SAM file" "

I have attached the igv.log file 

Thank you for your help,

Babs 

[Helga Thorvaldsdottir]

Hi Babs,

I saw from the log file that this file is in a shared iCloud Drive. I thought that might be an issue - we had never tried that. But I've just confirmed that loading bams from a shared iCloud Drive works just fine. The error you are getting is thrown by the low-level htsjdk library that we use to read the BAM file. It seems to think you have a SAM file, rather than a BAM file. But a quick google found that this error is sometimes thrown when the BAM file is corrupted.

Helga