Samantha (she/her)
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Hi WangZiwei, No problem, I'm happy to help! I'll take a look at the other articles and have them updated if necessary. If we can assist you with anything else, please let us know. Best, Samantha
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Hi WangZiwei, Thanks for bringing this up. I have brought this to our User Education team to update the "Somatic short variant discovery (SNVs + Indels)" article and have the GitHub links point t...
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Hi WangZiwei, Thanks for reaching out. You should refer to the WDL pipeline found in the broadinstitute/gatk repository (https://github.com/broadinstitute/gatk/tree/master/scripts/). Please let ...
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HI Jason Ni, Thank you for writing in about this issue. Can you share the workspace where you are seeing this issue with GATK/Terra Support by clicking the Share button in your workspace? The Share...
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Hi Kevin Meli, Thanks for reaching out. It looks like you've cloned a much older version of the GATK Somatic CNV workflow. The tools in the workflow have since been replaced, which is probably why ...
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Thanks, Philipp Hähnel. Wesley Kwong - are you able to resolve your issue with Philipp's advice? Best, Samantha
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I see. Can you temporarily share the gs://bruce-processed-data bucket with me (svelasqu@broadinstitute.org)? Even though the index file path isn't explicitly being passed to the GetPileupSummaries ...
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Hi Wesley Kwong, It looks like the error message in that submission is the one Genevieve pointed out in her latest message: A USER ERROR has occurred: Illegal argument value: Positional arguments w...
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Hi Wesley Kwong, Can you share the Submission ID so we can take a closer look at the issue? Best, Samantha
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Hi Oliver Ruebenacker, I've confirmed with the pipeline authors that the dbsnp file is indeed incorrect. I'll work on getting this updated in the featured workspace. Thank you for pointing this out...