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How to Understand SVCNVDiscovery result: CN "-1" value with CNQ "." value

Dear Genome STRiP users,

I got the CN and CNQ value by SVCNVDiscovery. After sorting the CNQ and the corresponding CN value, I found some weird CN values and CNQ values as below -- 10 samples out of 10686 samples (24 samples: CNQ (not .) < 13, and 24 samples: 13 < CNQ < 20).

ID sample 1 sample 2 sample 3 sample 4 sample 5
CNQ . . . 0.5 1.8
CN -1 -1 -1 2 2

So may I have your suggestions about:

  1. What does CN = -1 and CNQ = . mean? Does it mean that there are no confident copy number values?

  2. Whether 10 out of 10686 samples has -1 as CN value (24 samples: CNQ (not .) < 13, and 24 samples: 13 < CNQ < 20) is a good CNV calling or a bad calling?

  3. If this is a bad calling, may I have your suggestion about how to improve it, such as running in multiple batches (but more samples will make the estimation better?), using longer -intervalList in SVCNVDiscovery, or using longer -L in the SVPreprocess (if really cannot load the whole 94million cram file)?

Thank you very much.

P.S. It looks like that the ordered bulletin in this markdown window does not work so my post does not have the number order at the head of each question.

Best regards,
Wusheng

Answers

  • zhangwushengzhangwusheng Member

    Sorry, when I say "P.S. It looks like that the ordered bulletin in this markdown window does not work so my post does not have the number order at the head of each question.", it means that number order is not shown in the "preview" but can be shown after posting. So please ignore this "P.S.". :p

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    I'm a little surprised by the CN -1. Can you send me the full vcf record? (perhaps by email)

    As to whether the calling is good or bad (and in particular whether preprocessing on a small interval, which is not advised, is giving you suboptimal results) I would recommend looking at PlotGenotypingResults to start and focus especially on some examples of longer CNVs.

  • zhangwushengzhangwusheng Member

    Hi @bhandsaker ,

    Just sent my result by email. Thank you very much.

    Best regards,
    Wusheng

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