How do I obtain the known indel file for Trypanosoma congolense species?
Unfortunately, we cannot help you with that. You will have to do some searching for the known indel sites. If your organism does not have one, you can simply input your bam file into RealignerTargetCreator. You do not need to input a known indels file. The tool will use the reads in the bam file to find target intervals to realign.