The imputationbot Command-Line Utility

The imputationbot is a CLI utility to interact with imputation servers running Cloudgene 3 and Imputation Server 2, such as the TOPMed Imputation Server and the Michigan Imputation Server.

imputationbot is maintained by Lukas Forer. See the Contact Page for contact information.

Installation

1. Install Java (8 or higher).
2. Install curl.
3. Navigate to the folder where you want to install the app.
4. Run the following command:

   curl -sL imputationbot.now.sh/v2 | bash
   

   (this command downloads an installation script and immediately runs it).
5. Check if the imputationbot got installed correctly:

   imputationbot version
   

Using imputationbot

Register a Server

You can register a server by calling

imputationbot add-instance

This will start an interactive process that will ask you for the server URL and an API token. You can get your token from the server website: press on your name, then "Profile", then "Create API Token".

Submit a Job

You can submit a job by calling the impute subcommand. For example:

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

Note that you don't explicitly select the server. imputationbot automatically selects the first registered server that contains a refpanel with the given name.

Monitor Jobs

List all your jobs and their status:

imputationbot jobs

Get more details about one job:

imputationbot jobs <job-id>

Download Results

To download all output files for a given job, run:

imputationbot download <job-id>

If the job is not done, imputationbot waits until the job is finished and then downloads the files.

You can provide the decryption password to decompress the downloaded ZIP files directly:

imputationbot download <job-id> --password <my-password>