1. Community
2. New User Advice
3. Help with running GATK RNAseq workflow with docker backend and multiple cpus?

Hi ThyagoLC, The way you will want to configure your WDL will depend on where you are running it. If you are running on your local machine, the docker containers will have access to the available C...

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• Genevieve Brandt (she/her)
• September 03, 2021 17:13
• 1 vote

1. Community
2. Special GATK Use Cases
3. calling large scale structural variants

Hi lid.zigh, Calling structural variants uses multiple GATK tools so we have pipelines for this method. Our most up to date pipeline is uses WDL and can be found here: https://github.com/broadinsti...

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• Genevieve Brandt (she/her)
• August 31, 2021 18:32
• 1 vote

1. Community
2. Somatic
3. Incorrect Annotation from Funcotator

Hi Hanbing Song, This is a known issue with the Funcotator 1.7 data sources and the version of GATK you are using. See the github ticket and another user's post. You can upgrade your GATK version t...

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• Genevieve Brandt (she/her)
• August 26, 2021 17:45
• Edited
• 1 vote

1. Community
2. Germline
3. .GenomicsDBException: Duplicate sample name found:

Hi Nicholas Bailey, Unfortunately there is no way to remove the samples from the GenomicsDB workspace. This is why we recommend that users create a backup of the GenomicsDB workspace before updatin...

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• Genevieve Brandt (she/her)
• August 26, 2021 16:59
• 1 vote

1. Community
2. General Discussion
3. Multi-sample VCF for CNV calling

Thanks for the update Muhammad Shoaib Akhtar!

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• Genevieve Brandt (she/her)
• July 28, 2021 15:06
• 1 vote

1. Community
2. General Discussion
3. BQSR bootstrapping for multiple-sample dataset with no known variants (non-human)

Hi all, Thanks for the follow up question on this post so that we can address it! We don't have any current BQSR bootstrapping methods or recommendations for when there is no known sites file. If y...

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• Genevieve Brandt (she/her)
• July 21, 2021 21:10
• 1 vote

1. Community
2. General Discussion
3. RNA Mutect Pipeline

Hi D, Thanks for writing into the GATK forum! Our group does not support the pipeline you are referring to, it looks like it is made at the broad institute but it is not one of our featured workspa...

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• Genevieve Brandt (she/her)
• July 16, 2021 20:40
• 1 vote

1. Community
2. General Discussion
3. Orientation bias filter on germline analysis

Hi Alexandre Defelicibus, I think the orientation bias filter you are thinking of is part of FilterMutectCalls, which only works for somatic data. We wouldn't recommend you try this with germline d...

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• Genevieve Brandt (she/her)
• July 13, 2021 23:36
• 1 vote

1. Community
2. Germline
3. GenotypeGVCFs is too long

Hi Quentin Chartreux,  We have created a usage guidelines article for GenomicsDB that also applies when using GenotypeGVCFs with a GenomicsDB workspace: https://gatk.broadinstitute.org/hc/en-us/art...

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• Genevieve Brandt (she/her)
• July 13, 2021 18:13
• 1 vote

1. Community
2. Non-Human
3. Issues while running GenotypeGVCFs

There is some mention here in our glossary article: https://gatk.broadinstitute.org/hc/en-us/articles/360035891051-GenomicsDB Best of luck!

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• Genevieve Brandt (she/her)
• July 01, 2021 15:31
• 1 vote