I am sorry you are also having issues with the gautil functionality.
For precomputing BAM coverage using the "coverage" function of gautil, it will by default look for the reference sequence TSF file in the ../GenomeBrowse/Application/Data folder. If the reference file is saved in a different directory then you can use the --refFolder="folder location" command to point to the new location.
As an example if you had your BAM and index files (sample.bam and sample.bam.bai) stored on a network drive (M) and the reference file was stored on an external hard drive (G) then the command would look something like the following.
gautil coverage M:/sample.bam --refFolder="G:/" or ./gautil.exe coverage M:/sample.bam --refFolder="G:/" if you are on a Linux machine.
The tool will then pick out the correct reference TSF file to use for computing the coverage based on the chromosome names and lengths listed in the header of your BAM file. The names and lengths listed in the BAM must match exactly to what is listed in the TSF file for the coverage tool to be able to identify the correct reference.
Please let me know if you continue to have any issues. We will also look into improving the documentation for the gautil tool to be more comprehensive and accurate.