Merge branch 'master' into features/msav-support

.readthedocs.yml

@@ -0,0 +1,14 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+mkdocs:
+  configuration: mkdocs.yml

docs/workshops/ASHG2023.md

@@ -0,0 +1,27 @@
+**Workshop ASHG2023**
+
+# Welcome to the Michigan Imputation Server Workshop!
+
+## Workshop Title
+The Michigan Imputation Server: Data Preparation, Genotype Imputation, and Data Analysis
+
+## Topic 
+Statistical Genetics and Genetic Epidemiology
+
+## Target Audience 
+Attendees interested in learning how to perform genotype imputation and use imputed genotypes in their research, especially trainees. There are no prerequisites for this workshop. Attendees are expected to follow materials on their personal laptops.
+
+## Workshop Slides
+You can download the slides of all workshop sessions [here](https://github.com/genepi/imputationserver-ashg/raw/main/slides/MIS_Workshop_2023.pdf). Please also have a look at the individual sessions below for additional training material.
+
+## Links
+- [Interactive Poll](http://pollev.com/ashg)
+- [Workshop Website](https://www.ashg.org/meetings/2023meeting/2023-ashg-invited-workshop-schedule/)
+
+## Workshop Facilitator(s)
+- Christian Fuchsberger, christian.fuchsberger@eurac.edu (Eurac Research)
+- Sebastian Schönherr, sebastian.schoenherr@i-med.ac.at (Medical University of Innsbruck)
+- Lukas Forer, lukas.forer@i-med.ac.at (Medical University of Innsbruck)
+- Xueling Sim, ephsx@nus.edu.sg (National University of Singapore)
+- Saori Sakaue, ssakaue@broadinstitute.org (Broad Institute)
+- Albert Smith, albertvs@umich.edu (University of Michigan)

docs/workshops/ASHG2023/Session1.md

@@ -0,0 +1,18 @@
+**Workshop ASHG2023  > Session 1: Imputation and the Server**
+
+# Server Links
+
+[Michigan Imputation Server](https://imputationserver.sph.umich.edu)
+
+[TOPMed Imputation Server](https://imputation.biodatacatalyst.nhlbi.nih.gov)
+
+
+# Selected Literature
+
+[Das S, Forer L, Schönherr S, Sidore C, Locke AE, Kwong A, Vrieze SI, 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. Nat Genet. 2016 Oct;48(10):1284-1287. doi: 10.1038/ng.3656.](https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/27571263/)
+
+[Das S, Abecasis GR, Browning BL. Genotype Imputation from Large Reference Panels. Annu Rev Genomics Hum Genet. 2018 Aug 31;19:73-96. doi: 10.1146/annurev-genom-083117-021602.](https://arjournals.annualreviews.org/doi/10.1146/annurev-genom-083117-021602?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed)
+
+[Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics. 2015 Mar 1;31(5):782-4. doi: 10.1093/bioinformatics/btu704. Epub 2014 Oct 22. PMID: 25338720; PMCID: PMC4341061.](https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25338720/)
+
+[Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 2012 Jul 22;44(8):955-9. doi: 10.1038/ng.2354. PMID: 22820512; PMCID: PMC3696580.](https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22820512/)

docs/workshops/ASHG2023/Session2.md

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+**Workshop ASHG2023 > Session 2: Run a job, Data Preparation and Data Download**
+
+# Welcome
+
+Welcome to Session 2! In this session you will learn how to submit a job on Michigan Imputation Server (MIS) and how to prepare your input data that they are passing the QC step.
+
+# Tutorial
+
+## Getting Started
+As a quick start, the following video includes all required steps to submit and monitor a job using the graphical web interface.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/HMP76DpL_I0?si=GSFsFMbqJQFVUhJj" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+
+## Run a job on your own
+After you [registered](https://imputationserver.sph.umich.edu/start.html#!pages/register) successfully, the following URL will bring you directly to the job submission page:
+[https://imputationserver.sph.umich.edu/index.html#!run/minimac4](https://imputationserver.sph.umich.edu/index.html#!run/minimac4)
+
+## Submission Page - Select parameters
+The UI includes several parameters which need to be specified. Our [Getting Started guide](https://imputationserver.readthedocs.io/en/latest/getting-started/) describes all required parameters to do so.
+
+## Submission Page - Upload data
+
+We are providing two data datasets that can be downloaded from below. In case the unphased dataset is selected, an additional phasing step using Eagle is automatically performed. For this demo, we recommend selecting the **HapMap 2 panel** (Input parameter 'Reference panel') to get your results as quick as possible. Please also have a look at our [supported reference panels](https://imputationserver.readthedocs.io/en/latest/reference-panels/) when using MIS in a production setup.
+
+- [Phased dataset chr20 hg19](https://github.com/genepi/imputationserver-ashg/raw/main/files/chr20.R50.merged.1.330k.recode.small.vcf.gz)
+- [Unphased dataset chr20 hg19](https://github.com/genepi/imputationserver-ashg/raw/main/files/chr20.R50.merged.1.330k.recode.unphased.small.vcf.gz)
+
+## Submission Page - Submit
+After all parameters have been selected and you click 'submit', the job will be added to our Input Validation and QC queue. Please have a look at our [Data Preparation Guide](https://imputationserver.readthedocs.io/en/latest/prepare-your-data) to learn how to prepare your dataset using a pre-imputation tool.
+
+## Monitor Jobs, Download Data
+If the job passes the QC step, it will be added to our long-time queue. As soon as your job is finished, you will receive an email with the password to download and encrypt your data. Also checkout our [Pipeline Overview Guide](https://imputationserver.readthedocs.io/en/latest/pipeline/) to learn more about the different internal parameters. The complete source code can also be found on [GitHub](https://imputationserver.sph.umich.edu).
+
+## QC Results 
+A simple QC report including the frequency plot is available [here](https://htmlpreview.github.io/?https://github.com/genepi/imputationserver-ashg/blob/main/files/qcreport.html).
+
+
+# Contact
+If you have any questions please write [me an email](mailto:sebastian.schoenherr@i-med.ac.at) or contact me on [Twitter](https://twitter.com/seppinho).

docs/workshops/ASHG2023/Session3.md

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+**Workshop ASHG2023 > Session 3: Performing GWAS using imputed data**

docs/workshops/ASHG2023/Session4.md

@@ -0,0 +1,121 @@
+**Workshop ASHG2023 > Session 4: nf-gwas, Imputation Bot and PGS Server**
+
+# nf-gwas Report
+You can download a nf-gwas test report from [here](https://github.com/genepi/imputationserver-ashg/raw/main/files/nf-gwas-example.zip). Please unzip the file and open the index.html file.
+
+# Imputation Bot Tutorial
+
+## Requirements
+
+You will need the following things properly installed on your computer.
+
+* [Java 8 or higher](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
+
+
+## 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:
+
+```sh
+imputationbot version
+```
+
+The documentation is available at [http://imputationbot.readthedocs.io](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**:
+
+![Image1](/workshops/ASHG2020/images/token1.png)
+
+2. Click on **Create API Token**
+
+![Image1](/workshops/ASHG2020/images/token2.png)
+
+3. Copy your API Token and paste it when `imputationbot add-instance` ask for it.
+
+![Image1](/workshops/ASHG2020/images/token3.png)
+
+Api Tokens are valid for 30 days. You can check the status in the web interface or with `imputationbot instances`
+
+![Image1](/workshops/ASHG2020/images/token4.png)
+
+4. 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:
+
+```bash
+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](http://imputationbot.readthedocs.io).
+
+## Contact
+
+Feel free to contact [us](https://imputationserver.sph.umich.edu/index.html#!pages/contact) in case of any problems.

docs/workshops/ASHG2023/Session5.md

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+**Workshop ASHG2023 > Session 5: HLA Imputation**
+
+- [Example output of the HLA imputation VCF](https://github.com/genepi/imputationserver-ashg/raw/main/files/chr6.dose.vcf.gz)

docs/workshops/ASHG2023/Session6.md

@@ -0,0 +1 @@
+**Workshop ASHG2023 > Session 6: The TOPMed Imputation Server**

mkdocs.yml

@@ -1,7 +1,7 @@
 site_name: Michigan Imputation Server
 theme: readthedocs
 
-pages:
+nav:
 - Home: index.md
 - Getting Started: getting-started.md
 - Data Preparation: prepare-your-data.md
@@ -13,28 +13,17 @@ pages:
   - API: api.md
   - Docker: docker.md
   - Create Reference Panels: create-reference-panels.md
-- Workshops:
-  - ASHG2022:
-    - Overview: workshops/ASHG2022.md
-    - "Session 1: Imputation and the Server": workshops/ASHG2022/Session1.md
-    - "Session 2: Run a job, Data Preparation and Data Download": workshops/ASHG2022/Session2.md
-    - "Session 3: Performing GWAS using imputed data": workshops/ASHG2022/Session3.md
-    - "Session 4: Imputation Bot and PGS Server": workshops/ASHG2022/Session4.md
-    - "Session 5: HLA Imputation": workshops/ASHG2022/Session5.md
-    - "Session 6: TOPMed Imputation Server": workshops/ASHG2022/Session6.md
-  - ASHG2020:
-    - Overview: workshops/ASHG2020.md
-    - "Session 1: Imputation and the Server": workshops/ASHG2020/Session1.md
-    - "Session 2: Run a job, Quality Control and Data Preparation": workshops/ASHG2020/Session2.md
-    - "Session 3: Tracking runs and downloading data": workshops/ASHG2020/Session3.md
-    - "Session 4: Performing GWAS using imputed data": workshops/ASHG2020/Session4.md
-    - "Session 5: Imputation bot": workshops/ASHG2020/Session5.md
-    - "Session 6: TOPMed Imputation Server": workshops/ASHG2020/Session6.md
-    - "Session 7: Imputation panels": workshops/ASHG2020/Session7.md
+- ASHG2023:
+  - Overview: workshops/ASHG2023.md
+  - "Session 1: Imputation and the Server": workshops/ASHG2023/Session1.md
+  - "Session 2: Run a job, Data Preparation and Data Download": workshops/ASHG2023/Session2.md
+  - "Session 3: Performing GWAS using imputed data": workshops/ASHG2023/Session3.md
+  - "Session 4: nf-gwas, Imputation Bot and PGS Server": workshops/ASHG2023/Session4.md
+  - "Session 5: HLA Imputation": workshops/ASHG2023/Session5.md
+  - "Session 6: TOPMed Imputation Server": workshops/ASHG2023/Session6.md
 - Contact: contact.md
 
 
-
 repo_name: genepi/imputationserver
 repo_url: https://github.com/genepi/imputationserver
 edit_uri: edit/master/docs

pom.xml

@@ -296,7 +296,7 @@
 		<dependency>
 			<groupId>lukfor</groupId>
 			<artifactId>pgs-calc</artifactId>
-			<version>1.5.4</version>
+			<version>1.5.5</version>
 		</dependency>
 
 	</dependencies>

src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java

@@ -24,6 +24,7 @@
 
 public class ImputationPipeline {
 
+
 	public static final String PIPELINE_VERSION = "michigan-imputationserver-1.8.0-beta4";
 
 	public static final String IMPUTATION_VERSION = "minimac-v4.1.6";