gymreklab/str-toolkit repository overview

⁠STRTools

Toolkit for genome-wide analysis of STRs

⁠Docker

The Dockerfile in this container sets up a Docker with GangSTR and STRTools installed. You can pull this image from https://hub.docker.com/r/gymreklab/str-toolkit⁠.

⁠Install

Run the following command to install:

python setup.py install [--prefix=PREFIX]

to install locally, set --prefix=$HOME and ensure $HOME is on your PYTHONPATH.

⁠Tools

STRTools includes the following tools.

• dumpSTR: a tool for filtering VCF files with STR genotypes (from HipSTR⁠ or GangSTR⁠)
• plinkSTR: a tool for performing STR association studies
• mergeSTR: a tool to merge vcf files from gangSTR
• postmaSTR: a tool for post-processing and priotization of STR genotypes
• statSTR: a tool is used for computing stats on VCF files

Type <command> --help to see a full set of options.

⁠Usage

See the README in each subidrectory for usage details.

⁠Support

STRTools supports GangSTR v2.4 or newer. The required filtering tags are not available in the older versions of GangSTR.