Yuwei Bao
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Activity overview
Latest activity by Yuwei Bao-
Yuwei Bao commented,
Thank you very much!! That leads to a plot! However, I am not sure how to get rid of the extra genome. For example, the PlotDenoisedCopyRatios leads to the resultThese are the genomes I want to sho...
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Yuwei Bao commented,
Hi Gökalp:Thanks for your reply.Yes, I am using the sample.allelicCount.tsv file created by CollectAllelicCountsHere are the example entries of the DFG2.allelicCounts.tsv CONTIG POSITION RE...
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Yuwei Bao created a post,
PlotModeledSegments lead to java.lang.IllegalArgumentException related to inconsistency
Brief summary: When running non-human whole genome sequencing sample following somatic CNV pipeline (How to part II) Sensitively detect copy ratio alterations and allelic segments – GATK (broadinst...
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Yuwei Bao commented,
Hi Gökalp:Thank you very much for confirming! Could you recommend resources to understand and explain these CNV copy ratio results? I am new to CNV analysis. Running other pipelines results in the ...
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Yuwei Bao commented,
Hi Gökalp: Thank you very much for your response! I got it figured out. The step I did incorrectly was in the first step PreprocessIntervals. I want to share it here if others run into the same iss...
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Yuwei Bao created a post,
PlotDenoisedCopyRatios lead to empty result for non-human results
REQUIRED for all errors and issues: a) GATK version used: docker image spacecade7/tutorial_11682_11683:gatk4.0.1.1 b) Exact command used: docker run -v WORKDIR/./:WORKDIR/./ spacecade7/tutorial_1...
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Yuwei Bao created a post,
Reproduce GATK Tutorial#11682 leading to different results
REQUIRED for all errors and issues: a) GATK version used: docker image spacecade7/tutorial_11682_11683:gatk4.0.1.1b) Exact command used: tutorial1=./gatk_CNV/tutorial/tutorial_11682tutorial2=./ga...
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Yuwei Bao created a post,
Somatic CNV Workflow Tutorials
REQUIRED for all errors and issues: a) GATK version used: docker image: tutorial_11682_11683:gatk4.0.1.1 b) Exact command used: gatk --java-options "-Xmx3g" CollectAllelicCounts \ -I s...
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Yuwei Bao created a post,
Create Panel of Normals Issue
Hi everyone: I am using GATK v4.2.6.1 and I have trouble producing Panel of Normal for somatic mutation calling using the following workflow from the tutorial : Step 1: Run Mutect2 in tumor-only ...