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2. Non-Human
3. PlotModeledSegments lead to java.lang.IllegalArgumentException related to inconsistency

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
• June 26, 2024 16:16
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1. Community
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3. PlotModeledSegments lead to java.lang.IllegalArgumentException related to inconsistency

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
• June 26, 2024 05:19
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2. Somatic
3. Reproduce GATK Tutorial#11682 leading to different results

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
• June 25, 2024 14:45
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3. PlotDenoisedCopyRatios lead to empty result for non-human results

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
• June 25, 2024 14:39
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