1. Community
2. Special GATK Use Cases
3. Trio Denovo annotation using VariantAnnotator PossibleDenovo not working?

Hi Jan, I apologize for the delay in getting back to you. I was attending a conference. Can you please try the latest version of GATK which is v4.2.2.0. The version you are using is quite old at th...

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• Bhanu Gandham
• September 11, 2021 17:22
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• 0 votes

1. Community
2. General Discussion
3. HRun not found in vcf header or INFO

Hi Mingzhou Fu, I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK. You can read more about ou...

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• Bhanu Gandham
• August 30, 2021 17:56
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1. Community
2. Germline
3. genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file

Hi Diya, Please post the exact command you are using, the version of the tool and the entire error log. 

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• Bhanu Gandham
• August 07, 2021 01:59
• 0 votes

1. Community
2. General Discussion
3. MuTect2 Phasing tags (PGT:PID:PS:) in FORMAT column: How to avoid/remove them?

Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as this topic is for reporting bugs with GATK. You can read more about our forum guidelines and the top...

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• Bhanu Gandham
• June 25, 2021 03:49
• 0 votes

1. Community
2. General Discussion
3. Skipping Intel deflater in GATK

HI,   Unfortunately, we do not support GATK3 anymore. Please upgrade to the latest version of GATK4. Thank you!

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• Bhanu Gandham
• June 25, 2021 03:45
• 0 votes

1. Community
2. Special GATK Use Cases
3. Mutect2 for Pool-seq ?

Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as the non-human topic is for reporting bugs and issues with GATK. You can read more about our forum gu...

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• Bhanu Gandham
• June 14, 2021 14:36
• 0 votes

1. Community
2. Documentation Questions
3. MTLowHeteroplasmyFilterTool documentation

Hi ,   Thank you for your post. We are currently prioritizing bugs and errors with GATK tools. You can read more about our forum guidelines and the topics here: Forum Guidelines. We are tracking do...

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• Bhanu Gandham
• June 14, 2021 14:35
• 0 votes

1. Community
2. General Discussion
3. Recalibrated output (BQSR)

Hi Maggie,  These values look normal to me. Take a look at this article for detailed documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-B...

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• Bhanu Gandham
• June 04, 2021 22:00
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• 0 votes

1. Community
2. Non-Human
3. GenotypeGVCF too many genotypes

Hi Victoria Buswell For pooled samples our recommendation is to use Mutect2. Can you try to use Mutect2 instead of HaplotypeCaller for your variant calling and let me know if that works better? 

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• Bhanu Gandham
• June 04, 2021 15:44
• 0 votes

1. Community
2. Non-Human
3. bqsr output issue

Hi Maggie Sudo Pui San   Can you please start a new thread with your question. Please post the exact commands you are using and the versions of tools you are using. Can you also pease give an expla...

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• Bhanu Gandham
• June 03, 2021 17:40
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• 0 votes