Pamela Bretscher
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Recent activity by Pamela Bretscher Sort by recent activity-
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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Hi Jugpreet Singh, I just wanted to check in. Have you been able to run CombineGVCFs successfully? Kind regards, Pamela
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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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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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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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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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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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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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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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Okay, sounds good!