STRipy - ExpansionHunter's catalogue creator

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.

Create variant catalogue from a BED file

Convert a BED file to variant catalogue

You can use a BED file or tab/space delimited text file with maximum of 250 thousand 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:

chrX	67545316	67545385	GCA
chr4	3074876	3074933	CAG	HTT
chr9	69037286	69037304	GAA	FXS

Available loci

Loci in the catalogue

Catalogue's content

Reference genome

hg38 / GRCh38

hg19 / GRCh37

Chromosome naming

Use "chr" prefix in chromosome names (e.g. when using hg38 or hg19 genome)

Extended analysis

Include off-target regions (allows to genotype long alleles*, but slowers the time of analysis and may overestimate the length of repeats)

* 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).