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Toolkit for genome-wide analysis of STRs
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.gitignore adding init files to package Feb 20, 2019
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README.md

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

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

Usage

See the README in each subidrectory for usage details.

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