/imputationbot

Automate interactions with the imputation servers :robot:

Primary LanguageJavaMIT LicenseMIT

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imputation-bot

GitHub release build Documentation Status

Automate interactions with Michigan Imputation Servers

Requirements

You will need the following things properly installed on your computer.

  • Java 8 or higher

Download and Install

Linux or macOS

Download and install the latest version from our download page using the following commands:

curl -sL imputationbot.now.sh | bash

It will create the imputationbot executable file in the current directory. Optionally, move the imputationbot file to a directory accessible by your $PATH variable.

Test the installation with the following command:

imputationbot version

The documentation is available at http://imputationbot.readthedocs.io.

You can also download the latest version of imputationbot-X.X.X-macos.zip or imputationbot-X.X.X-linux.zip from our download page.

Windows

Download the latest version of imputationbot-X.X.X-windows.zip from our download page.

  • Open the zip file and extract the exe file to a folder of choice

  • Open the command-line and navigate to your folder

  • Test the installation by running the following command:

imputationbot version

The documentation is available at http://imputationbot.readthedocs.io.

Get your API Token

Enable API access from your Profile page.

  1. Login and click on your username and then profile:

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  1. Click on Create API Token

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  1. Copy your API Token and paste it when imputationbot add-instance ask for it.

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Api Tokens are valid for 30 days. You can check the status in the web interface or with imputationbot instances

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  1. Next, configure imputationbot with the following command:
imputationbot add-instance

imputation-bot 1.0.0 🤖
https://imputationserver.sph.umich.edu
(c) 2019-2020 Lukas Forer, Sebastian Schoenherr and Christian Fuchsberger
Built by lukas on 2020-09-01T11:31:10Z

Imputationserver Url [https://imputationserver.sph.umich.edu]:
API Token [None]: eyJjdHkiOiJ0ZXh0XC9wbGFpbiIsImFsZyI6IkhTMjU2In0.eyJtYWlsIjoibHVrYXMuZm9yZXJAaS1tZWQuYWMuYXQiLCJleHBpcmUiOjE1NzMyMjkwNTY3NTEsIm5hbWUiOiJMdWthcyBGb3JlciIsImFwaSI6dHJ1ZSwidXNlcm5hbWUiOiJsdWtmb3IifQ.qY7iEM6ul-gJ0EuHmEUHRnoS5hZs7kD1HC95NFaxE9w

Run imputation

You can use the impute command to submit a job:

  • The --files parameter defines the location of our VCF file. If we plan to impute more than one file we can enter the path to a folder or separate multiple filenames by ,.
  • We can use the --refpanel parameter to specify the reference panel. For the 1000 Genomes Phase 3 panel we use 1000g-phase-3-v5. If we are not sure what panels are provided by the server, we can use imputationbot refpanels to get a list of all reference panels and their supported populations.
  • For --population we use eur which stands for European

The complete command looks like this:

imputationbot impute --files /path/to/your.vcf.gz --refpanel 1000g-phase-3-v5 --population eur

A test file is available here.

After submission we get the URL where we can monitor the progress of our job.

Monitor Jobs

However, we can also use imputation-bot to get a list all our jobs and their status:

imputationbot jobs

To get more details about our job, we can use the jobs command followed by the job ID:

imputationbot jobs job-XXXXXXXX-XXXXXX-XXX

Download all Results

We can use the download command to download all imputed genotypes and the QC report at once:

imputationbot download job-XXXXXXXX-XXXXXX-XXX

If the job is still running, imputation-bot waits until the job is finished and starts automatically with the download.

You can provide imputation-bot the password we sent you via email and it decrypts all files for you:

imputationbot download job-XXXXXXXX-XXXXXX-XXX --password MYPASSWORD

Documentation

The documentation is available at http://imputationbot.readthedocs.io.

Contact

Feel free to contact us in case of any problems.