Create a custom variant catalogue for ExpansionHunter. You can either convert a BED file containing any STR loci to a variant catalogue or select manually pick known pathogenic loci from the list you wish to target during your analysis.
You can use a BED file or tab/space delimited text file with maximum of ~1 million loci to convert it to variant catalogue. You must have each locus on a new line, where the columns are: 1) chromosome, 2) STR start position, 3) STR end position, 4) repeat unit, and 5) locus ID (optional). If the locus ID is missing, then the ID will be composed from the reference coordinates.