Getting started
To use imputation-bot you have to enable API access from your Profile page. The required API token can be obtained from the Michigan Imputation Server or TOPMed Imputation Server website. You can find configuration instructions here.
Run imputation
You can use the impute
command to submit a job:
- The
--files
parameter defines the location of your VCF file(s). If you plan to impute more than one file you can enter the path to a folder or multiple filenames separated by space. - The
--refpanel
parameter specifies the used reference panel. For the 1000 Genomes Phase 3 panel the ID is1000g-phase-3-v5
. If you are not sure what panels are provided by the server, you can useimputationbot refpanels
to get a list of all reference panels and their supported populations. - The
--population
parameter is used in quality control to compare the allele frequencies between your data and the reference panel. Please note that not every reference panel supports all sub-populations. For 1000 Genomes Phase 3 you can useeur
which stands for European.
The complete command using this example file looks like this:
imputationbot impute --files chr20.small.vcf.gz --refpanel 1000g-phase-3-v5 --population eur
After submission we get the URL where we can monitor the progress of our job.
Auto download
If the --autoDownload
flag is set then imputation-bot waits until the job is finished and starts the download for you:
imputationbot impute --files chr20.small.vcf.gz --refpanel 1000g-phase-3-v5 --population eur --autoDownload
A new folder is created in the current directory and contains all the downloaded results.
Auto download and decryption
You can can combine the --autoDownload
flag with the --password
parameter to set a user-defined password to encrypt the result files. In this case imputation-bot decrypts all files after download:
imputationbot impute --files chr20.small.vcf.gz --refpanel 1000g-phase-3-v5 --population eur --autoDownload --password my_strong_password
The output directory contains now also all *.vcf.gz
and *.info.gz
files.
Submit all files from a folder
imputationbot impute --files folder/with/vcf-files --refpanel 1000g-phase-3-v5 --population eur
Submit only vcf.gz files
imputationbot impute --files folder/*.vcf.gz --refpanel 1000g-phase-3-v5 --population eur
Learn more about the impute
command here.
Monitor jobs
We can also use Imputation Bot to get a list of 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
Learn more about the jobs
command here.
Download results
We can use the download
command to download all imputed genotypes and the QC report at once for a given job ID:
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
Learn more about the download
command here.