How to explain the CNV result produced by GAKT4

I've got the CNV result produced by GATK4, but I can't understand it. As you see, the value of 'Segment_Mean' in the second line nearly equal to which in the third line, but why the result of 'Segment_Call' are so different. Can anyone explain it for me? The result as following :
Sample Chromosome Start End Num_Probes Segment_Mean Segment_Call
test chr13 32890740 32972912 21 0.999514914665561 -
test chr17 41197878 41267873 14 0.999792077464719 0

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Answers

  • aaroncaaronc Cambridge, MAMember

    Hi Yujian,

    I'm guessing the confidence bounds on these segments are extremely tight and so even this tiny difference it falls below the threshold for the copy-neutral state.

    It's possible this is an error-mode of your data, but it's not possible to diagnose without more information. Would it be possible to post the plot from your output? (Keeping in mind that this forum is public)

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