1. Community
2. Special GATK Use Cases
3. GATK-SV GenotypeBatch: svtk count error

Hi Arosato, Our GATK Support team on this forum supports the GATK-SV single sample featured workspace on Terra. We are not able to support individual cromwell instances for our WDLs. You can see ou...

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• Genevieve Brandt (she/her)
• April 20, 2022 20:25
• 1 vote

1. Community
2. General Discussion
3. BwaMemIndexImageCreator:: Expected running time for 1 TB db

I'm glad the resources are helpful! Let us know if you have other questions.

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• Genevieve Brandt (she/her)
• April 13, 2022 17:42
• 1 vote

1. Community
2. General Discussion
3. Can I know the progress of Haplotypecaller?

Hi JE S, HaplotypeCaller does not estimate the time remaining, but you can view the progress in the progress meter, which will appear in the standard output by the tool. Let me know if you have any...

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• Genevieve Brandt (she/her)
• April 13, 2022 03:06
• 1 vote

1. Community
2. General Discussion
3. Discrepancy between GATK joint vcf and recaled.bam files

Hi Xiao Ran Luo, Thanks for writing into the forum! I have a few key suggestions that might help you to make sense of what is going on with your samples. We have a troubleshooting document that go...

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• Genevieve Brandt (she/her)
• April 13, 2022 03:05
• 1 vote

1. Community
2. General Discussion
3. BwaMemIndexImageCreator:: Expected running time for 1 TB db

Hi Renald James Legaspi, The pre-built database is within the pathseq resource bundle hosted on google cloud platform: gs://gatk-best-practices/pathseq/resources/.  A 1 TB database can easily take ...

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• Genevieve Brandt (she/her)
• April 12, 2022 19:53
• 1 vote

1. Community
2. New User Advice
3. GATK working, but -ERC command not found

Hi Ann W, Thanks for trying out GATK! Thankfully, I think this error can be easily solved. It looks like it's just a small typo in your command line so that the -ERC line is read as a different com...

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• Genevieve Brandt (she/her)
• April 12, 2022 16:50
• 1 vote

1. Community
2. New User Advice
3. Picard CrosscheckFingerprints not identifying samples from the same individual as a MATCH

Hi Christopher Sisk, Thanks for writing in about this question! Hopefully we can help to figure out why you are seeing this. First, something to know, is that contaminated samples can erroneously b...

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• Genevieve Brandt (she/her)
• April 07, 2022 22:01
• 1 vote

1. Community
2. General Discussion
3. BwaMemIndexImageCreator:: Expected running time for 1 TB db

Thanks Renald James Legaspi for the update. It does look like it's still actively running so let it keep running for now and I'll reach out to Mark Walker regarding the 64 GB db. 

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• Genevieve Brandt (she/her)
• April 07, 2022 21:10
• 1 vote

1. Community
2. General Discussion
3. Tumor in Normal contamination

Hi Ibel Carri, 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...

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• Genevieve Brandt (she/her)
• April 06, 2022 01:33
• 1 vote

1. Community
2. General Discussion
3. Discrepancy between GATK joint vcf and recaled.bam files

Hi Xiao Ran Luo, 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 ...

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• Genevieve Brandt (she/her)
• April 06, 2022 01:30
• 1 vote