Unlike SNPs, INDELs don't have a unique way of representing a mutation. Depending on the underlying reference sequence, one INDEL could be written in dozens of different ways. To facilitate comparison between men, it is useful to write the all the mutations in a standard form. The standard I'm using here is to ensure that the last base in the REF and ALT values for an INDEL are different, and that the first base is the same. I include at least one base in both the REF and ALT values for the INDEL.
This is the complete list of replace rules applied to all imported kits, both BigY and FGC Elite. For each new kit that is added, it is necessary to add new rules for INDELs found in that kit.