.. _UTILITIES:

Command-Line Tools
===========================

TRTools offers a variety of command-line tools for performing manipulations to TR genotype VCFs.
(These tools have 'STR' in their name, but are applicable to all TR VCFs).

.. toctree::
   :maxdepth: 1
   :name: source
   :hidden:

   source/dumpSTR.rst
   source/statSTR.rst
   source/qcSTR.rst
   source/compareSTR.rst
   source/mergeSTR.rst
   source/associaTR.rst
   source/prancSTR.rst
   source/simTR.rst
   source/annotaTR.rst

.. Include directives from tool READMEs

.. include:: ../trtools/dumpSTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/mergeSTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/qcSTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/statSTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/compareSTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/associaTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/prancSTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/simTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

.. include:: ../trtools/annotaTR/README.rst
   :start-after: overview_directive
   :end-before: overview_directive_done   

:doc:`source/dumpSTR`

* |dumpSTR overview|

:doc:`source/statSTR`

* |statSTR overview|

:doc:`source/qcSTR`

* |qcSTR overview|

:doc:`source/compareSTR`

* |compareSTR overview|

:doc:`source/mergeSTR`

* |mergeSTR overview|

:doc:`source/associaTR`

* |associaTR overview|

:doc:`source/prancSTR`

* |prancSTR overview|

:doc:`source/simTR`

* |simTR overview|

:doc:`source/annotaTR`

* |annotaTR overview|