Re: [svtoolkit-help] CNV detection in pedigrees

[Bob H. <han...@br...>]

Hi, Oliver,

The relatedness shouldn't cause any problem.
Genome STRiP doesn't have any mode that is specific to trios or related 
individuals, so you can use Mendelian violations as a QC metric.
When you do this, you should take into account the quality of each 
genotype call (e.g. CNQ).
CNQ is phred-scaled, so a CNQ of 13, for example, corresponds to 95% 
confidence and is where we generally set our default filters for calling 
a variant site.
However, at 95% confidence you would still expect occasional mendel 
errors, but you should see them decrease if you look only at genotypes 
with higher confidence thresholds.

-Bob

On 2/17/15, 6:10 PM, Homann, Oliver wrote:
>
> Hello,
>
> I'm hoping to use STRiP for CNV detection in support of a sequencing 
> project.   After looking over the documentation, I find myself unsure 
> of whether it is appropriate for my dataset.  Specifically, I have 
> ~100 samples covering 10 pedigrees, and wonder whether the 
> inter-relatedness of some of the samples would impact SV modeling and 
> detection.  Any guidance you can offer would be much appreciated.
>
> Regards,
>
> Oliver Homann
>
>
>
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