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Copy file name to clipboardExpand all lines: README.md
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This repository contains the Imputation Server 2 workflow to facilitate genotype imputation at scale. It serves as the underlying workflow of the [Michigan Imputation Server](https://imputationserver.sph.umich.edu).
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## Citation
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> Das S*, Forer L*, Schönherr S*, Sidore C, Locke AE, Kwong A, Vrieze S, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C. Next-generation genotype imputation service and methods. Nature Genetics 48, 1284–1287 (2016).
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> Das S*, Forer L*, Schönherr S*, Sidore C, Locke AE, Kwong A, Vrieze S, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C. Next-generation genotype imputation service and methods. Nature Genetics 48, 1284–1287 (2016).
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<sub>*Shared first authors</sub>
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## License
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[Version 2.0.11](https://github.com/genepi/imputationserver2/releases/tag/v2.0.11) - Add threads parameter to compression
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[Version 2.0.7 - 2.0.10](https://github.com/genepi/imputationserver2/releases/tag/v2.0.9) - Fix chrX renaming issue for clouds and enhance error/status messages
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[Version 2.0.3 - Version 2.0.6](https://github.com/genepi/imputationserver2/releases/tag/v2.0.6) - Fix QC issues and remove HTSJDK index creation for input validation and QC.
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[Version 2.0.2](https://github.com/genepi/imputationserver2/releases/tag/v2.0.2) - Set minimac4 tmp directory (required for larger sample sizes).
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|`name`| The label of the population. (e.g. EUR) |
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|`samples`| Number of samples in the reference panel |
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Note: the population id has to be the same as in the legend files.
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Note: the population id has to be the same as in the sites files.
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#### Quality Filters
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### Example YAML
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Here's an example YAML configuration for a reference panel. This configuration describes a reference panel named "HapMap 2" for an Imputation Server, including details about its version, data sources, and populations represented. The files are stored on AWS S3 and are directly consumed by the pipeline from there.
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Here's an example YAML configuration for a reference panel. This configuration describes a reference panel named "HapMap 2" for an Imputation Server, including details about its version, data sources, and represented populations. The files are stored in subdirectories of the application and can be consumed by the pipeline from there.
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```yaml
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name: HapMap 2
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description: HapMap2 Reference Panel for Imputation Server
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name: HapMap 2 (GRCh37/hg19)
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description: HapMap2 Reference Panel for Michigan Imputation Server
A full example of a reference panel, including all data and the cloudgene.yaml, can be downloaded [here](https://imputationserver.sph.umich.edu/resources/ref-panels/imputationserver2-hapmap2.zip).
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### Note on `$chr` Variable
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In the example YAML configuration provided, you may have noticed the presence of the `$chr` variable in some URLs. This variable is a placeholder for the chromosome number and will be replaced by the Nextflow pipeline.
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### Legend Files
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### Sites Files
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A site file is a tab-delimited file consisting of 8 columns: **ID**, **CHROM**, **POS**, **REF**, **ALT**, **AAF_EUR**, **AAF_ALL**, **MAF_EUR**, and **MAF_ALL**. The first five columns (**ID**, **CHROM**, **POS**, **REF**, and **ALT**) are required, while the **Allele Frequency (AAF)** and **Minor Allele Frequency (MAF)** columns are optional.
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A legend file is a tab-delimited file consisting of 5 columns (`id`, `position`, `a0`, `a1`, `all.aaf`).
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The optional **AAF** and **MAF** columns provide allele frequency information for different populations supported by the reference panel. Specifically, **AAF_EUR** and **MAF_EUR** represent allele frequencies for the European population, while **AAF_ALL** and **MAF_ALL** represent allele frequencies for all populations combined.
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---
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- Open [http://localhost:8082](http://localhost:8082)
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- Login with default admin account: username `admin` and password `admin1978`
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- Imputation can be tested with the following [test file](https://github.com/genepi/imputationserver2/raw/main/tests/input/chr20-phased/chr20.R50.merged.1.330k.recode.small.vcf.gz)
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- Imputation can be tested with the following [test file](https://github.com/genepi/imputationserver2/raw/main/tests/data/input/chr20-phased/chr20.R50.merged.1.330k.recode.small.vcf.gz)
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### Default Configuration
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}
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```
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3. Got to Settings -> General and set Workspace to "S3" and enter the location of a subfolder in an S3 bucket. Enter the location of a subfolder in an S3 bucket. Currently, it must be a subfolder; a bucket won't work (Example: `s3://cloudgene/workspace`).
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3. Go to Settings -> General and set Workspace to "S3" and enter the location of a subfolder in an S3 bucket. Enter the location of a subfolder in an S3 bucket. Currently, it must be a subfolder; a bucket won't work (Example: `s3://cloudgene/workspace`).
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Optional add [Wave](https://www.nextflow.io/docs/latest/wave.html) and [Fusion](https://www.nextflow.io/docs/latest/fusion.html) support to improve performance:
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### Activate mail support
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- Configure mail server in Settings -> General -> Mail
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- Configure Nextflow to use Cloudgenes mail settings by add the following to the global configuration (Settings -> General -> Nextflow) or adapt/create files `config/nextflow.confing` (see [Nextflow Documention](https://www.nextflow.io/docs/latest/config.html#config-mail) for all available mail settings)
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- Configure Nextflow to use Cloudgenes mail settings by add the following to the global configuration (Settings -> General -> Nextflow) or adapt/create files `config/nextflow.config` (see [Nextflow Documentation](https://www.nextflow.io/docs/latest/config.html#config-mail) for all available mail settings)
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```
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mail {
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### Adapt default parameters
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Parameters can be changed in the `nextflow.config`` file of the application. Example:
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Parameters can be changed in the `nextflow.config` file of the application. Example:
Copy file name to clipboardExpand all lines: cloudgene.hla.yaml
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description: "<p> Thank you for using our multi-ethnic HLA imputation panel, built from ~20,000 whole genome sequencing samples from five global populations. </p> <p>
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Please cite this manuscript if you would like to include imputed results from the panel in your work: </p> <p>
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Luo, Y., Kanai, M., Choi, W., Li, X., Yamamoto, K., Ogawa, K., Gutierrez-Arcelus, M., Gregersen, P. K., Stuart, P. E., Elder, J. T., Fellay, J., Carrington, M., Haas, D. W., Guo, X., Palmer, N. D., Chen, Y.-D. I., Rotter, J. I., Taylor, K. D., Rich, S., … Raychaudhuri, S. (2020). <b> A high-resolution HLA reference panel capturing global population diversity enables multi-ethnic fine-mapping in HIV host response</b>. https://doi.org/10.1101/2020.07.16.20155606 <br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>). </p>"
Copy file name to clipboardExpand all lines: cloudgene.pgs.yaml
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id: imputationserver2-pgs
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name: Polygenic Score Calculation
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description: "You can upload genotyped data and the application imputes your genotypes, performs ancestry estimation and finally calculates Polygenic Risk Scores.<br><br>No dataset at hand? No problem, download our example dataset: <a href=\"https://imputationserver.sph.umich.edu/resources/50-samples.zip\" class=\"btn btn-sm btn-secondary\" style=\"color:#ffffff !important\"><i class=\"fa fa-file\"></i> 50-samples.zip</a><br><br>"
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id: imputationserver2
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name: Genotype Imputation
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description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
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- Start cloudgene server: `./cloudgene server`
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- Open [http://localhost:8082](http://localhost:8082)
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- Login with default admin account: username `admin` and password `admin1978`
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- Imputation can be tested with the following [test file](https://github.com/genepi/imputationserver2/raw/main/tests/input/chr20-phased/chr20.R50.merged.1.330k.recode.small.vcf.gz)
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- Imputation can be tested with the following [test file](https://github.com/genepi/imputationserver2/raw/main/tests/data/input/chr20-phased/chr20.R50.merged.1.330k.recode.small.vcf.gz)
body "Dear ${params.user.name}, \n Your job has been ${statusMessage}.\n\n More details can be found at the following link: ${params.service.url}/index.html#!jobs/${params.project}"
body "Dear ${params.user.name},\n${statusText}\n\nMore details can be found at the following link: ${params.service.url}/index.html#!jobs/${params.project_id}"
subject "[${params.service.name}] Job ${params.project} is complete"
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body "Dear ${params.user.name},\n Your imputation job has finished succesfully. The password for the imputation results is: ${params.encryption_password}\n\n You can download the results from the following link: ${params.service.url}/index.html#!jobs/${params.project}"
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body "Dear ${params.user.name},\nYour imputation job has finished succesfully. The password for the imputation results is: ${params.encryption_password}\n\nYou can download the results from the following link: ${params.service.url}/index.html#!jobs/${params.project_id}"
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}
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println"::message:: Data have been exported successfully. We have sent a notification email to <b>${params.user.email}</b>"
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} else {
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sendMail{
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to "${params.user.email}"
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subject "[${params.service.name}] Job ${params.project} is complete"
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body "Dear ${params.user.name},\n Your PGS job has finished successfully.\n\n You can download the results from the following link: ${params.service.url}/index.html#!jobs/${params.project}"
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body "Dear ${params.user.name},\nYour PGS job has finished successfully.\n\nYou can download the results from the following link: ${params.service.url}/index.html#!jobs/${params.project_id}"
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}
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println"::message:: Data have been exported successfully. We have sent a notification email to <b>${params.user.email}</b>"
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} else {
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println"::message:: Data have been exported successfully."
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