Analysis of STRs using STR catalogs

The most straightforward and common way to use the STR catalog is to estimate the sizes of STRs using ExpansionHunter. Expansion Hunter is a tool to estimate STR sizes based on short reads data, and the json format of the catalog can be directly used by ExpansionHunter.

Usage

For detailed usage about ExpansionHunter, you can refer to the ExpansionHunter documentation. Briefly, you only need the BAM/CRAM file from the sample you need to analyze and the fasta file of the reference genome. Catalogs can be found in either hg19 or hg38 depending on the reference.

After getting all the files ready, simply run

ExpansionHunter --reads <BAM/CRAM file with aligned reads> \
                --reference <FASTA file with reference genome> \
                --variant-catalog <JSON file specifying variants to genotype> \
                --output-prefix <Prefix for the output files>

Running time

For the genome-wide catalog, it is preferred to use streaming mode in ExpansionHunter v5.0.0 in multi-thread mode so it can be analyzed quickly.