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I obtained very large copy numbers (e.g., 115) in the CN column of .call.cns output file, which is not logical. Is there anyone who could help clarify why I got this large number as CN in the output?
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Hello,
I encountered a problem while running the cnvkit.py batch command for a normal sample in a tumor-only mode. This is the command I used:
cnvkit.py batch ~/CNV/normal_sample.bam -p 12 --fasta ~/CNV/hg19.fa --seq-method wgs --normal --annotate ~/CNV/refFlat.txt --output-dir ~/CNV --scatter --diagram &> ~/CNV/normal_sample.cnvkit.log
I obtained very large copy numbers (e.g., 115) in the CN column of .call.cns output file, which is not logical. Is there anyone who could help clarify why I got this large number as CN in the output?
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