1. Community
2. General Discussion
3. Resource bundle hg38 hosts corrupted VCF

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

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• Bhanu Gandham
• June 03, 2021 17:29
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1. Community
2. General Discussion
3. identify heteroplasmic variants MTLowHeteroplasmyFilterTool

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

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• Bhanu Gandham
• June 03, 2021 17:28
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3. VariantFiltration MQRankSum error: "-12.5 is not a recognized option"

Hi Chloé Girard I think you might have missed that last step of sending us the files. The instructions on how to send us the files are provided in the article mentioned above.

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• Bhanu Gandham
• May 20, 2021 15:51
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1. Community
2. General Discussion
3. VariantFiltration MQRankSum error: "-12.5 is not a recognized option"

Hi Chloé Girard   Can you please share with me the reference you are using and the vcf file? I would like to recreate this error on my end to figure out why this is happening. Please follow instruc...

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• Bhanu Gandham
• May 14, 2021 17:53
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1. Community
2. General Discussion
3. Error in document

Hi ,   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 the GATK tools. You can read more about o...

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• Bhanu Gandham
• May 14, 2021 17:49
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1. Community
2. General Discussion
3. [HaplotypeCaller] Seeing only 1 thread on GCP instance

Hi , 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 our forum gui...

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• Bhanu Gandham
• May 07, 2021 19:09
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1. Community
2. General Discussion
3. VariantFiltration MQRankSum error: "-12.5 is not a recognized option"

Hi Chloé Girard Hi For what you are trying to do use VariantFiltration over SelectVariants. Also there are some other corrections to made in the command you are using: --filter-expression is used...

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• Bhanu Gandham
• April 30, 2021 20:40
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• 0 votes

1. Community
2. General Discussion
3. Slow execution of PathseqPipelineSpark

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
• April 30, 2021 20:30
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1. Community
2. Special GATK Use Cases
3. LiftoverVCF Model Organism Issue

Hi , I am going to move your post into our Community Discussions -> Special GATK Use Cases topic, as the Non-Human topic is for reporting bugs and issues with GATK. You can read more about our foru...

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• Bhanu Gandham
• April 23, 2021 18:56
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1. Community
2. Somatic
3. GenomicsDBImport does not support GVCFs with MNPs

Hi Rodolfo Adrián Arriaga Rivera   This issue has been solved on the forum already. Take a look at this thread: https://gatk.broadinstitute.org/hc/en-us/community/posts/360058358051-HaplotypeCaller...

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• Bhanu Gandham
• April 23, 2021 18:52
• 0 votes