Seunghun Han
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Hi, the notebook links in "2. Towards ascertaining the quality of gCNV calls, use Jupyter Notebook" section seem to have been broken. Is there a way to access these notebooks?
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Thanks a lot!!! This is exactly what I need. Best,Seunghun
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Hi Samantha (she/her),Is there any update on this? thanks,Seunghun
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I'm using broadinstitute/gatk:latest docker to run DoC.
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I don't think it has anything to do with the way I'm viewing the file. This is how it looks when I opened on of the gene level summary on VIM.I don't have outputs from GATK3 and GATK4 DoC runs on a...
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Both interval level and gene level summary outputs have this. The screenshot above was from gene level summary output
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Hi Genevieve, I checked IGV and gene summary records for multiple transcripts and it looks like the numbers make sense. I think I will just go ahead and modify the refseq gene list so that each gen...
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Hi, I'm having the same issue, and I'm using a refseq gene list generated by following this article - https://gatk.broadinstitute.org/hc/en-us/articles/360035532032-RefSeq-gene-list-formatSo the re...
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Hi, I was using DepthOfCoverage from GATK-3.7 before, and after I updated it to the one from latest GATK, I'm getting individual gene level summary for each gene transcript for a gene when I use th...