HipSTR-references

Reference files for running HipSTR with various organisms

Getting Started

HipSTR requires a BED file containing the STR regions to genotype. We've generated these files for various organisms and assemblies as listed in the table below:

Organism	Assembly	URL
Human	hg19	https://github.com/HipSTR-Tool/HipSTR-references/raw/master/human/hg19.hipstr_reference.bed.gz
Human	hg38	https://github.com/HipSTR-Tool/HipSTR-references/raw/master/human/hg38.hipstr_reference.bed.gz
Human	GRCh37	https://github.com/HipSTR-Tool/HipSTR-references/raw/master/human/GRCh37.hipstr_reference.bed.gz
Human	GRCh38	https://github.com/HipSTR-Tool/HipSTR-references/raw/master/human/GRCh38.hipstr_reference.bed.gz
Mouse	mm10	https://github.com/HipSTR-Tool/HipSTR-references/raw/master/mouse/mm10.hipstr_reference.bed.gz

To use a particular file with HipSTR, download it and decompress it using gzip. For instance, if you are interested in the BED file for humans for the hg19 assembly:

wget https://github.com/HipSTR-Tool/HipSTR-references/raw/master/human/hg19.hipstr_reference.bed.gz
gunzip hg19.hipstr_reference.bed.gz

The file hg19.hipstr_reference.bed is then ready to use as input to HipSTR's --regions option.

Building the references

For both mouse and human, we've provided detailed information about how we built each reference in this repository. If you're interested in learning more, please checkout the human or mouse subdirectories.

The human HipSTR reference

Other organisms

If you're interested in a file for a different model organism, send us an email at [email protected] and we'll be happy to help build one