TRTools: a toolkit for genome-wide tandem repeat analysis

TRTools includes a variety of utilities for filtering, quality control and analysis of tandem repeats downstream of genotyping them from next-generation sequencing. It supports multiple recent genotyping tools (see below).

See full documentation and examples at

If you use TRTools in your work, please cite: Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek. (2020) TRTools: a toolkit for genome-wide analysis of tandem repeats. Bioinformatics. (


Note: TRTools supports Python versions 3.8 and up. We do not officially support python version 3.7 as it is end of life, but we believe TRTools likely works with it from previous testing results.

With conda

conda install -c conda-forge -c bioconda trtools

Optionally install bcftools which is used to prepare input files for TRTools (and ART which is used by simTR) by running:

conda install -c conda-forge -c bioconda bcftools art

With pip

First install htslib (which contains tabix and bgzip). Optionally install bcftools. These are used to prepare input files for TRTools and aren’t installed by pip.

Then run:

pip install --upgrade pip
pip install trtools

Note: TRTools installation may fail for pip version 10.0.1, hence the need to upgrade pip first

Note: if you will run or test simTR, you will also need to install ART. The simTR tests will only run if the executable art_illumina is found on your PATH. If it has been installed, which art_illumina should return a path.

From source

To install from source (only recommended for development) clone the TRTools repository from github and checkout the branch you’re interested in:

git clone -b master
cd TRTools/

Now, create 1) a conda environment with our development tools and 2) a virtual environment with our dependencies and an editable install of TRTools:

conda env create -n trtools -f dev-env.yml
conda run -n trtools poetry install

Now, whenever you’d like to run/import pytest or TRTools, you will first need to activate both environments:

conda activate trtools
poetry shell

With Docker

Please refer to the biocontainers registry for TRTools for all of our images. To use the most recent release, run the following command:

docker pull


TRTools includes the following tools.

  • mergeSTR: a tool to merge VCF files across multiple samples genotyped using the same tool

  • dumpSTR: a tool for filtering VCF files with TR genotypes

  • qcSTR: a tool for generating various quality control plots for a TR callset

  • statSTR: a tool for computing various statistics on VCF files

  • compareSTR: a tool for comparing TR callsets

  • associaTR: a tool for testing TR length-phenotype associations (e.g., running a TR GWAS)

  • prancSTR: a tool for identifying somatic mosacisim at TRs. Currently only compatible with HipSTR VCF files. (beta mode)

  • simTR: a tool for simulating next-generation sequencing reads from TR regions. (beta mode)

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

It additionally includes a python library, trtools, which can be accessed from within Python scripts. e.g.:

import trtools.utils.utils as stls
allele_freqs = {5: 0.5, 6: 0.5} # 50% of alleles have 5 repeat copies, 50% have 6
stls.GetHeterozygosity(allele_freqs) # should return 0.5


We recommend new users start with the example commands described in the command-line interface for each tool. We also suggest going through our vignettes that walk through some example workflows using TRTools.

Supported TR Callers

TRTools supports VCFs from the following TR genotyping tools:

See our description of the features and example use-cases of each of these tools.


After you’ve installed TRTools, we recommend running our tests to confirm that TRTools works properly on your system. Just execute the following:

Development Notes

  • TRTools only currently supports diploid genotypes. Haploid calls, such as those on male chrX or chrY, are not yet supported but should be coming soon.

Contact Us

Please submit an issue on the trtools github


We appreciate contributions to TRTools. If you would like to contribute a fix or new feature, follow these guidelines:

  1. Consider discussing your solution with us first so we can provide help or feedback if necessary.

  2. Install TRTools from source as above.

  3. Fork the TRTools repository.

  4. Create a branch off of master titled with the name of your feature.

  5. Make your changes.

  6. If you need to add a dependency or update the version of a dependency, you can use the poetry add command.

    • You should specify a version constraint when adding a dependency. Use the oldest version compatible with your code. Don’t worry if you’re not sure at first, since you can (and should!) always update it later. For example, to specify a version of numpy>=1.23.0, you can run poetry add 'numpy>=1.23.0'.

    • Afterwards, double-check that the poetry.lock file contains 1.23.0 in it. All of our dependencies should be locked to their minimum versions at all times. To downgrade to a specific version of numpy in our lock file, you can explicitly add the version via poetry add 'numpy==1.23.0', manually edit the pyproject.toml file to use a >= sign in front of the version number, and then run poetry lock --no-update.

  7. Document your changes.

    If applicable, update the REAMDEs in the directories of the files you changed with new usage information.

    • New doc pages for the website can be created under <project-root>/doc and linked to as appropriate.

    • If you have added significant amounts of documentation in any of these ways, build the documentation locally to ensure it looks good.

    cd to the doc directory and run make clean && make html, then view doc/_build/html/index.html and navigate from there

  8. Add tests to test any new functionality. Add them to the tests/ folder in the directory of the code you modified.

    • cd to the root of the project and run poetry run pytest --cov=. --cov-report term-missing to make sure that (1) all tests pass and (2) any code you have added is covered by tests. (Code coverage may not go down).

    • cd to the root of the project and run nox to make sure that the tests pass on all versions of python that we support.

  9. Submit a pull request (PR) to the master branch of the central repository with a description of what changes you have made. Prefix the title of the PR according to the conventional commits spec. A member of the TRTools team will reply and continue the contribution process from there, possibly asking for additional information/effort on your part.

    • If you are reviewing a pull request, please double-check that the PR addresses each item in our PR checklist


If you are a TRTools maintainer and wish to publish changes and distribute them to PyPI and bioconda, please see PUBLISHING.rst in the root of the git repo. If you are a community member and would like that to happen, contact us (see above).

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