BAM File Visualization

[Dale Annear]

Hello

I am having an issue visualizing the BAM files generated through the lobSTR alignment step in software such as IGV. However, this is not the case when I align the same FASTQ files through BWA. I have attached a screenshot of an example where the two different BAM files are opened alongside each other in the IGV software.

I see in the original lobSTR paper in Figure 2.C that the alignment is visualised very nicely. Would you be able to advise on how to achieve this? Thanks!

Kind regards,

Dale