# Agent $$\textit{001}$$

## 1. Introduction

Agent is a tool for genome-wide association studies (GWAS) using the agent file format. It can convert between the bgen and agent formats and run a GWAS on genotypes in the agent format.

## 2. Changes

• June 1st 2021. Initial release of Agent 001.

## 3. Source

Available at the git repository.

Available at the git repository.

## 5. Manual

Agent 001 build 4e7bc94601, February 2020.
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AGENT         https://agent.engineering/
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Copyright 2020, Winfield Chen and Lloyd T. Elliott.

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USAGE
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• agent --version Prints version and build information.
• agent --help Prints this software manual.
• agent --genotypes 〈GFILE〉 〈DESTINATION〉 Converts the genotype file specified by 〈GFILE〉 (in bgen[2] format) to the .a1 genetic file format.
• agent --genotypes 〈GFILE〉 --phenotypes 〈PFILE〉 〈DESTINATION〉 Runs a GWAS using the genotype file specified by 〈GFILE〉 (in agent format) and the phenotype file specified by 〈PFILE〉 with output directory 〈DESTINATION〉.
• --genotypes〈GFILE〉Path to a genotype file in agent format.
• --phenotypes〈PFILE〉Path to a phenotype file.

TBA

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│ UNPACK    │
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TBA

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│ ERRORS    │
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The number of phenotypes specified in〈PFILE〉must be a multiple of the page size divided by 8. On most systems, the page size is 4096 bytes, and so the number of phenotypes must be a multiple of 512. If this condition is not met, then Agent will print an error message and exit.

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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

## 6. Citation

If you use Agent 001, or if this work inspires you to add compression based on source coding theory to your own population genetics software and pipelines, please cite TBA. You may send email correspondence to winfield ․ chen ᘒ sfu ․ ca or lloyd ․ elliott ᘒ sfu ․ ca.

## 7. References

If you use Agent 001, or if this work inspires you to add compression based on source coding theory to your own population genetics software and pipelines, please cite TBA. You may send email correspondence to winfield ․ chen ᘒ sfu ․ ca or lloyd ․ elliott ᘒ sfu ․ ca.