How to Visualize unmapped bam generated from GATK FastqToSam?

Question

[pragnapcu]

I have generated an unmapped bam file using GATK FastqToSam but cannot visualize it with IGV. What should be done?

Answer 1

[GenoMax]

By definition an "unmapped" BAM will contain fastq reads that are not mapped. They are simply converted to SAM format. So how can you visualize that file in IGV since the reads are not aligned to a reference?

If you simply want to look at the contents of the file you can do that with less/cat file.sam (if the file is in SAM format).

[pragnapcu]

So silly of me. Thank you GenoMax