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The GATK community forum is a place to resolve GATK issues, discuss with other GATK users around the globe, and find resources to help you while using GATK. Please follow these forum guidelines so that you can get the most out of this forum.
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Before You Post
The quickest way to get an answer to your question is if it already exists!
- Read the relevant tool documentation to find information about the recommended usage and possible issues.
- Read through our other documentation:
- Technical Documentation: Contains Troubleshooting GATK4 Issues, Glossary, and Algorithms
- Getting Started: Contains Best Practices Workflows, Tutorials, Computing Platforms, FAQs
- Validate your input files with ValidateSamFile for BAM/SAM files and ValidateVariants for VCFs.
- Search the forum for someone with the same issue. You can use our search function or use the power of Google by searching “site:gatk.broadinstitute.org” followed by your question.
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Writing a New Post
Couldn’t find a solution from the steps above? Make a new post! Read these instructions to determine the category of your post and what information we need so that you can get your question answered:
1. GATK Errors
An error message from a GATK Tool that is not a User Error, looks like a possible bug, or you can not debug yourself because it has not been previously discussed on the forum.
Please include:
- GATK and Java version numbers
- Complete GATK Command
- Complete Stack Trace [use --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' to see the entire stack trace]
- What previous methods you followed (Are you following the GATK Best Practices?)
- Descriptions of the troubleshooting steps you have already tried
2. Abnormal Results from GATK Tools
When you receive results from GATK tools that are not expected and you have tried our published troubleshooting steps.
Please include:
- GATK and Java version numbers
- Complete GATK Command
- What previous methods you followed (Are you following the GATK Best Practices?)
- Relevant details about your analysis
- Descriptions of what troubleshooting steps you have tried
- Illustrative examples of the issue you are seeing including an example of the results you expect
- e.g. attach IGV screenshots or give example variants
3. General Questions, Community Discussions, Feature Requests
All forum posts that do not fall into the above categories fall into this category. Please post these in the Community Discussions section in the relevant topic.
- Explain your use case so other people know if they have the same experience
- Clearly state what you know already and what you are trying to determine (what documentation are you already familiar with?)
- Give all relevant GATK information (example commands, troubleshooting information)
- Interact with posts that already exist! Let us know if there are feature requests you support or try to find information from users who have posted about your same question in the past. If there are popular posts in the Community Discussion section of the forum, our team will make sure to address these topics!
GATK Support Policy
Our support team aims to give excellent support to the GATK community, providing solutions to issues and helping users learn more about GATK tools.
Our number one priority is to help you troubleshoot tool errors and abnormal results. These could be from bugs in the code itself, or a problem with how you are using the tool. Either way, post these questions to the “Bug and Issue Reports” topics section. We ask that you be as specific as possible when you post the question and try to find possible solutions in our documentation (Before You Post).
Our second priority is to moderate community discussions and to help users learn more about GATK Tools. Our “Community Discussions” section covers a wide range of topics that we will monitor (however, not as regularly as the “Bug and Issue Reports” section). We generally are able to respond to these questions within 2-3 weeks, but some questions are harder for us to answer and take longer than others. We do not guarantee solutions to requests in this section, but all requests will be noted and compiled as we improve our resources and tools. The topics in this section are:
- General Discussion
- Documentation Questions
- New User Advice
- Special GATK Use Cases (Information here covers items that are not in the best practices but may someday be a part of the best practices)
- Webinar Discussions
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5 comments
Hello, Genevieve
I have a question that I'm using gatk to call snp of my samples, but the organism has no known snp database, so I can't perform the BQSR. And I read some recommendation for it, mainly including 2 solution: ①just to skip the BQSR,②to create a confifent snp database and use it for BQSR. However, the latter will take much time as I have a big number of sample. So I want to skip the BQSR, meanwhile, use hard filtering instead of VQSR to get my finnal vcf. I just want to know whether this solution is correct? and whether the information in final vcf file is credible if I perfoemed like this?
Genevieve Brandt (she/her) I can't access form for GATK guru. It says you need permission. Please fix it.
Thanks for the heads up Muhammad Shoaib Akhtar! I think I fixed it, please let me know if it works.
Genevieve Brandt (she/her) I'm sorry it didn't work. Following is error.
This form can only be viewed by users in the owner's organization.
Try contacting the owner of the form if you think this is a mistake. Learn More.
It's fixed now! Thanks for your interest Muhammad Shoaib Akhtar!
https://docs.google.com/forms/d/e/1FAIpQLSfEGzzqHdyDDU0dlARGieDd3pI_I9Q2YDXJfwtHeHhEu_QOQw/viewform?usp=sf_link
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