GATK2 tutorial » History » Revision 3
Revision 2 (Bryan Cosca, 03/16/2015 03:23 PM) → Revision 3/5 (Bryan Cosca, 03/16/2015 07:53 PM)
h1. Running GATK2 using Arvados This tutorial demonstrates how to run the GATK Unified Genotyper pipeline using GenomeAnalysisTK-2.2-16 from the Broad Institute. WIP h2. Uploading data through the web and using it on Arvados # In your home project, click on the blue *+ Add data* button in the top right. # Click *Upload files from my computer* # Click *Choose Files* and choose one set of paired end fastq files you would like to run GATK2 on. # Once you're ready, click *> Start* # Feel free to rename your Collection so you can remember it later. Click on the pencil icon in the top left corner next to *New collection* # Once that is uploaded, navigate back to the dashboard and click on *Run a pipeline...* and choose GATK2 / exome PE fastq to snp [dev] [public]. # You can change the input by clicking on the *[Choose]* button next to the *Sample FASTQ reads*. # Click on the dropdown menu, click on your newly-created project, and choose your desired input collection. Click *OK* and *Run* to run lobSTR v.3 on your data! WIP h2. Uploading data through your shell and using it on Arvados Full documentation can be found "here":http://doc.arvados.org/user/tutorials/tutorial-keep.html # Install the "Arvados Python SDK":http://doc.arvados.org/sdk/python/sdk-python.html on the system from which you will upload the data (such as your workstation, or a server containing data from your sequencer). Doing so will install the Arvados file upload tool, arv-put. # To configure the environment with the Arvados instance host name and authentication token, see "here":http://doc.arvados.org/user/reference/api-tokens.html # Navigate back to your Workbench dashboard and create a new project by clicking on the Projects dropdown menu and clicking Home. # Click on [+ Add a subproject]. Feel free to edit the Project name or description by clicking the pencil to the right of the text. # To add data, return to your shell, create a folder, and put the two paired-end fastq files you want to upload inside. Use the command arv-put * --project-uuid qr1hi-xxxxx-yyyyyyyyyyyyyyy. The qr1hi tag can be found in the url of your new project. This ensures that all the files you would like to upload are in one collection. # The output value xxxxxxxxxxxxxxxxxxxx+yyyy is the Arvados collection locator that uniquely describes this file. # Once that is uploaded, navigate back to the dashboard and click on *Run a pipeline...* and choose GATK2 / exome PE fastq to snp [dev] [public]. # You can change the input by clicking on [Choose] next to the *Sample FASTQ reads*. # Click on the dropdown menu, click on your newly-created project, and choose your desired input collection. Click *OK* and *Run* to run GATK2 on your data! WIP h3. FAQ WIP