Workshop ASHG2020 > Session 5: Imputation Bot

Slides

Learn how to use Imputation bot to automate job submission and interactions with imputation servers.

Download (pdf)

Tutorial

Requirements

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

Download and Install

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

curl -sL imputationbot.now.sh | bash

Test the installation with 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 0.8.3 🤖
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 Geneoms 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

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.