1. Community
2. Germline
3. The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*

Hi Oliver, Sorry for the delayed response. It does seem like there is an error in the Featured Workspace where the ref_name input for the 2-1-Processing-For-Variant-Discovery-B37 workflow is incorr...

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• Samantha (she/her)
• May 04, 2022 15:14
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1. Community
2. Germline
3. The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*

Hi Oliver Ruebenacker, Are you running the workflow on Terra? If so, can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? T...

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• Samantha (she/her)
• April 25, 2022 19:05
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1. Community
2. Germline
3. B37 joint variant calling workflow says "for hg38 only"

Hi Oliver Ruebenacker, Sorry for the delayed response. I've asked the WDL developers about this and they informed me that that comment is there as a disclaimer that the workflow hasn't been tested ...

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• Samantha (she/her)
• April 22, 2022 20:34
• 0 votes

1. Community
2. General Discussion
3. ScatterIntervalList error message when running DRAGEN-GATK on HPC

Hi NawarDalila, Sorry for the delayed response. Can you confirm whether you are still receiving this error after running the pipeline using the correct interval_list reference files mentioned in yo...

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• Samantha (she/her)
• January 25, 2022 21:33
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2. Germline
3. Sharded VCFs are not merged into final combined VCF file

Hi Georgi Hudjashov, Sorry for the confusion. It looks like the link in that article you mentioned needs to be updated. I'll put in a documentation request to get that changed. However, the workspa...

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• Samantha (she/her)
• November 02, 2021 15:42
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1. Community
2. Germline
3. Sharded VCFs are not merged into final combined VCF file

Hi Georgi Hudjashov,   Thanks for reaching out. It looks like you are referencing an outdated workspace, as indicated in the dashboard:   The new workspace with the most up-to-date workflows can b...

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• Samantha (she/her)
• October 29, 2021 16:28
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1. Community
2. Germline
3. Input configuration for GATK4-gCNV workflow on Terra

Hi Seunghun Han, The contig_ploidy_priors and intervals inputs are something you need to generate (with with WES data you'll need to start with the list of targets provided by the capture kit manuf...

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• Samantha (she/her)
• September 21, 2021 20:09
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2. Germline
3. Input configuration for GATK4-gCNV workflow on Terra

Hi Seunghun Han, Thanks for writing in. We'll take a look at your question and get back to you as soon as we can. Best, Samantha

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• Samantha (she/her)
• September 17, 2021 17:57
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1. Community
2. General Discussion
3. How do I import my data into notebook for germline filtering?

Hi J LoPiccolo, GenomicsDBImport does run in the 1-4-JointGenotyping-HG38 workflow as the ImportGVCFs task.  https://github.com/broadinstitute/warp/blob/20dbe7e7c602c116203523055da3399dbee9b399/tas...

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• Samantha (she/her)
• August 24, 2021 14:20
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1. Community
2. General Discussion
3. Avoid re-doing STAR references in RNAseq Germline variant workflow

Hi ThyagoLC, Thanks for following up and posting your solution! Best, Samantha

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• Samantha (she/her)
• August 12, 2021 15:15
• 0 votes