Toolkit for genome-wide analysis of STRs
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.
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.
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
Type <command> --help to see a full set of options.
See the README in each subidrectory for usage details.
STRTools supports GangSTR v2.4 or newer. The required filtering tags are not available in the older versions of GangSTR.