Does the IGV accept .bai file?

[liusimim]

In the Alignment in Bioconductor exercises, the task 7 was to visualize the results in IGV. However, when I import the BAM index files generated in the previous task into IGV, it didn't work and send me the message as follow. The BAM files worked well.

Does IGV only accept BAM files but not BAM index files?

[ThomasCarroll]

hi,

The BAM file contains the alignment read information so we should just load this.
The bai file contains index information for the corresponding BAM and is used by IGV to load reads from regions of interest within the BAM file.

The bai file should not be loaded directly in IGV.

thanks

tom