How To Build A Reference Exome Set When Detecting Cnvs With Exomedepth

Question

[siyu]

If I want to use the ExomeDepth to detect CNV, how can I to build a reference exome set ? Do I need a sample that may not contain the CNV I want to detection ? That is to say , I should get the two exome sequencing at the same time ??

Answer 1

[Vincent]

Yes the exomes that are part of the reference set should not contain the same CNV. If this is the case you cannot detect the CNV of interest of course. So if you deal with a family you want to exclude related individuals.

And ideally all these exomes (the test one and the reference exomes) should all have been generated as part of the same sequencing batch. You can try with exomes generated in different batches but the resulting CNV calls are likely to be much less accurate.

If these conditions are met, ExomeDepth should be able to build a good exome reference set by combining the most appropriate exomes (that is what the function select.reference.set does).

[siyu]

Thanks! I got it .

[yyaobo]

Searched a while for asking help of using exomeDepth, I thought this would be the best place. I have two questions related to the use of the software:

1: How many reference exomes I should use: on the same batch I have 30 samples, should I use as most samples as possible as references or just 5 - 10 of them according to the manual?

2: After I selected the reference panel with the code:

my.choice <- select.reference.set (test.counts = my.test, reference.counts = my.reference.set, bin.length = (ExomeCount.dafr$end - ExomeCount.dafr$start)/1000, n.bins.reduced = 10000)

and printed selected samples with print(my.choice[[1]]), I got only two samples names printed out, but there are ten samples in my.reference.set. How could this happen? There were 3 identical warning messages while computing the likelihoods and fitting the model:

Warning message: In aod::betabin(data = data, formula = as.formula(formula), random = ~1, : The data set contains at least one line with weight = 0.

Maybe because I am still a beginner of R, I can not understand the warning message. Could you help me to clarify it please?

Thanks a lot.

[Gerardo]

I have the same issue now, were you able to solve it?