I try to use Snap aligner (snap.cs.berkeley.edu/) and view the result in Igv for some viruses.
Here is the Snap output:
After that, I use samtools to index and sort the .sam file for .bam and .bam.bai. (They are not 0 bytes.)
I added the links to Igv (js) and this is what I see:
The files I used are working in Bowtie for example, so they cannot be the problem.
What am I missing here?