1. Community
2. Germline
3. workspace.haplotype_database_b37

Hi Oliver Ruebenacker, It looks like the "haplotype_database_b37 file that you're looking for is present on the "Workspace Data" tab of this workspace rather than within the b37Human reference data...

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• Pamela Bretscher
• April 07, 2022 18:24
• 0 votes

1. Community
2. Special GATK Use Cases
3. Error using CombineGVCFs - Exception thrown at Chr

Hi Jugpreet Singh, I just wanted to check in. Have you been able to run CombineGVCFs successfully? Kind regards, Pamela

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• Pamela Bretscher
• April 01, 2022 18:25
• 0 votes

1. Community
2. General Discussion
3. What intervals were used to create GATK's reference panel of normals for WGS CNV calling?

Hi Tracy Ballinger, Okay, thank you for clarifying and I'm glad that you were still able to find the intervals. At the moment, I don't believe we have documentation about explicitly how the panel o...

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• Pamela Bretscher
• April 01, 2022 13:14
• 0 votes

1. Community
2. Germline
3. erro running "gatk seq-format-validation workflow"

Hi Tomasz .P, Can you please check the contents of the "/gatk/cromwell-executions/ValidateBamsWf/1754f8db-da10-440c-bd04-591832dd8e44/call-ValidateBAM/shard-0/execution/stderr" file. This file shou...

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• Pamela Bretscher
• March 31, 2022 18:58
• 0 votes

1. Community
2. Somatic
3. How to create Panel of Normals?

Hi Tanay Biswas, Thank you for taking a look at those documents and trying this out. Could you please try increasing the specified memory for the GenomicsDBImport job using the -xmx option? Given t...

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• Pamela Bretscher
• March 31, 2022 13:31
• 0 votes

1. Community
2. Other
3. Error in GenomicsDBImport: Invalid deflate block found

HI Cristian Gonzalez-Colin, Thank you for working through this suggestion and finding the problematic sample. There are a few things you can try to pinpoint the issue with this donor and attempt to...

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• Pamela Bretscher
• March 29, 2022 16:37
• 0 votes

1. Community
2. Somatic
3. How to create Panel of Normals?

Hi Tanay Biswas, Okay, thank you for providing this. It does look like the issue is the GenomicsDBImport step which isn't producing the output that you are expecting. It looks like this is a memory...

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• Pamela Bretscher
• March 28, 2022 16:19
• 0 votes

1. Community
2. Germline
3. GATK v4.2.4.0 VariantAnnotator running too slow

Hi Riad Hajdarevic, I just wanted to update you on my discussion with some other members of the GATK team on this issue. It seems that the long runtime is likely just due to the sheer number of var...

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• Pamela Bretscher
• March 28, 2022 15:53
• 0 votes

1. Community
2. Somatic
3. How to create Panel of Normals?

Hi Tanay Biswas, Based on this output from CreateSomaticPanelofNormals, it looks like it might not be finished running. If you haven't received any error or output, is it possible that the job is j...

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• Pamela Bretscher
• March 25, 2022 14:00
• 0 votes

1. Community
2. Special GATK Use Cases
3. Error using CombineGVCFs - Exception thrown at Chr

Okay, sounds good!

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• Pamela Bretscher
• March 25, 2022 13:56
• 0 votes