1. Community
2. Germline
3. GenotypeGVCFs : VariantQueryProcessorException

Hi Henri-Jean, Thank you for writing into the GATK forum for this issue! It does seem like a strange error message, I haven't seen it before. What tool did you use to create these GVCFs? If it was ...

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• Genevieve Brandt (she/her)
• December 01, 2022 18:21
• 0 votes

1. Community
2. General Discussion
3. GetPileupSummaries error

Ok thank you, I am deleting the other post since it is a duplicate. We'll get back to you with a solution shortly!

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• Genevieve Brandt (she/her)
• December 01, 2022 17:48
• 0 votes

1. Community
2. Other
3. Invalid or corrupt jarfile error

Hi Benjamin Singer, Thanks for writing into the forum with this issue! Most likely there was something wrong when you tried to install gatk. We don't maintain conda or bioconda so I can't determine...

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• Genevieve Brandt (she/her)
• December 01, 2022 03:37
• 0 votes

1. Community
2. Somatic
3. GenomicsDBImport error: USER ERROR has occurred: Duplicate sample: 1. Sample was found in both file:

LG in the example you gave, both SM (sample names) are the same SM = 2. Could you clarify why you have two bam files with the same sample? You should merge these bam files before the Mutect2 step i...

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• Genevieve Brandt (she/her)
• December 01, 2022 03:33
• 0 votes

1. Community
2. General Discussion
3. GetPileupSummaries error

Tanay Biswas, is this other post the same issue? https://gatk.broadinstitute.org/hc/en-us/community/posts/10641300753819-GetPileupSummaries-malformed-header

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• Genevieve Brandt (she/her)
• December 01, 2022 03:28
• 0 votes

1. Community
2. General Discussion
3. expected variants not in active region by haplotypeCaller

Thank you for your post, Joseph! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Germline topic is for r...

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• Genevieve Brandt (she/her)
• December 01, 2022 03:27
• 0 votes

1. Community
2. New User Advice
3. Scatter Gather principle by chromosome on Gatk

Thank you for your post, Sushant! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.  Please see our Support Policy for more...

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• Genevieve Brandt (she/her)
• December 01, 2022 03:25
• 0 votes

1. Community
2. General Discussion
3. GenomicsDBImport doesn't work with >2 samples

Hi Tomás, We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up wh...

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• Genevieve Brandt (she/her)
• December 01, 2022 03:21
• 0 votes

1. Community
2. General Discussion
3. HaplotypeCaller fails at regions of high depth

Hi ulitskyi, I noticed that you already uploaded data. We require that you wait until a support team member asks you before you upload data. With that being said, I am wondering what happens when y...

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• Genevieve Brandt (she/her)
• November 23, 2022 03:48
• 0 votes

1. Community
2. General Discussion
3. Can GATK pipelines be used for Ion torrent data?

Hi DHWANI DHOLAKIA, Thank you for writing into the forum with your question and your patience while we got back to you. Yes, you can run GATK on Ion torrent data. Unfortunately, we are not experts ...

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• Genevieve Brandt (she/her)
• November 23, 2022 00:02
• 0 votes