Building a custom VCF, Reference Region and Locus Structure

[RoanS77]

Hello,
I am currently trying to build a custom VCF file that includes a series of regions of interest to be run by ExpansionHunter.

I retrieved the Reference Regions by running ExpansionHunterDeNovo outlier analysis and turning the output coordinates into TRF coordinates via UCSC Table Browser.

I had a few questions regarding how to handle some cases:

• The first one is which locus structure should I use for the VCF file? The one proposed by EHDN or the one given by TRF? The results of these two methods vary a lot, so I have to decide which is the best option.
• In case TRF returns more than one region after giving it EHDN coordinates, which one should I keep in the Reference Region of the VCF? All of them, just one, a set spanning the majority of the area or something else?

I will be available for further clarifications.
Thank you!