Oliver Ruebenacker
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Activity overview
Latest activity by Oliver Ruebenacker-
Oliver Ruebenacker commented,
Hello Genevieve, Thanks for the update and I'm looking forward to the results of the test! We've also looked deeper into the issue, and we noticed that while the variant called by GATK looked like ...
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Oliver Ruebenacker commented,
Hello, I reran it with "b37", but I'm still getting this error. Any ideas? Thanks! 2022/05/07 20:07:54 Starting container setup. 2022/05/07 20:07:56 Done container setup. 2022/05/07 20:07:58 Starti...
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Oliver Ruebenacker commented,
Hello, I was wondering if there is any update on this? Thanks! Best, Oliver
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Oliver Ruebenacker commented,
Hello, The workspace is here: https://app.terra.bio/#workspaces/amp-dcc-rfp15/Pollak_Nephrotic_Syndrome_Portal The submission with the error is here: https://app.terra.bio/#workspaces/amp-dcc-rfp15...
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Oliver Ruebenacker commented,
Thanks, looking forward!
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Oliver Ruebenacker commented,
Hello, For 2-1-Processing-For-Variant-Discovery-B37, the input "hg38" for ref_name looks suspicious. Is it incorrect and is the correct value "b37"? Could this be the cause for the error? Thanks! B...
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Oliver Ruebenacker commented,
Hello, I used GATK Best Practices workflows from beginning to end, including using the reference data that were provided with these workflows. If the references are inconsistent, how can this be ca...
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Oliver Ruebenacker created a post,
The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*
Hello, I've been using GATK Best Practices for Germline SNPs & Indels, workflow 2-4-JointGenotyping-B37 (after running the preceding ones), and after running for a week, the following two tasks fai...
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Oliver Ruebenacker created a post,
B37 joint variant calling workflow says "for hg38 only"
AnsweredHello, Your featured workspace has a workflow for joint variant calling for b37, but the WDL itself has a comment that it is "for hg38 Whole Genomes and Exomes (has not been tested on hg19)" (see b...
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Oliver Ruebenacker created a post,
workspace.haplotype_database_b37
Hello, I'm trying to run a clone of this workflow configuration:https://app.terra.bio/#workspaces/help-gatk/GATK4-Germline-Preprocessing-VariantCalling-JointCalling/workflows/help-gatk/2-4-JointGen...