Amateur problem here:
We know that it is possible to use the ExpansionHunter tool to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat. Here is the reference link: https://github.com/Illumina/ExpansionHunter
Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. Fragile X Syndrome, ALS, and Huntington's Disease are well known examples.
But I have encountered some difficulties dealing with ExpansionHunter.
I ask: is it possible to search for repetitions using other software, such as IGV (Integrative Genomics Viewer) for example or any other equivalent software?