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cn.mops calling copy number 1 state as CNV using the haplocn.mops function in an haploid WGS

Hi,

I use cn.mops to detect CNVs from WGS data of an haploid genome using the haplocn.mops function . However, I obtain CNVs of copy number 1, which should not be the case since the normal should be 1. I do not get any calls of copy number 2.

Does this function still assume a normal state of 2 despite it being suggested useful for haploid genome?

Would greatly appreciate any clarification on this.

Joan

genome sequencing r
• 3,043 views • link
updated by Ram Ram • written by jebet.joan • jebet.joan

1 answer

Hello Joan,

Yes, this can happen in rare cases. The reason is that the CNV calls and the integer copy numbers are made on different segments - I'll try to explain:

The CNV call joins consecutive segments with high or low signed informative/non-informative call. Let us assume that you have joined 4 segments that had: + / - / - / +. On this joined segments the integer copy numbers (CN) are called. It can happen that the probability of CN1 is slightly higher than CN2 - in this case the software returns CN2. You can check the posterior probabilities of the copy numbers for each segment, if you use "returnPosterior=TRUE".

I hope this helps - you can contact me also via email!

Regards,
Günter Klambauer

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updated by Ram Ram • written by klambauer • klambauer

I am in the same situation. Could you please explain this in greater detail? I am getting many of such calls and I am not sure how to prevent this behavior. Thanks a lot.

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updated by Ram Ram • written by Biomonika (Noolean) Biomonika (Noolean)

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