ExpansionHunter's catalogue creator

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.

Convert a BED file to variant catalogue

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.

Example content of a regions file:
chrX6754531667545385GCA
chr430748763074933CAGHTT
chr96903728669037304GAAFXS
 
Available loci
Loci in the catalogue
Catalogue's content
Reference genome
Chromosome naming
Extended analysis

* While off-target regions enables to genotype alleles longer than the fragment length, there is also a chance of getting overestimated genotypes (probably locus dependent). Interpret your results with a caution!

Known issues with using the catalogue and ExpansionHunter (v4.0.2 & v5.0.0):
• ARX_1 and ARX_2 as well as HOXA13_1, HOXA13_2 and HOXA13_3 tracts are too close to each other and false positive results for these loci may be received (you might want to only consider spanning reads).
• Genotypes returned for Replaced and Nested types of repeats also includes the non-pathogenic repeats. You could use STRipy to determine the presence of the pathogenic motif in your sample.
• Long homozyogus alleles (approximately above 500 bp) are likely determined as heterozyous with one allele being overestimated and the other underestimated.
Additional issues with ExpansionHunter v4.0.1 or an earlier version: genotyping AR, ATXN1 and TCF4 loci are limited to the read length (approximately).