Hi Guru,

It is possible to run exomeCopy without any calculated background read
depth, using the GC content variables and the 'width' variable supplied to
the X.names argument of exomeCopy().

Even better would be if you could find a few samples of "healthy" exomes
which used the same enrichment kit as your dataset. By generating
background from publicly downloaded exomes (we used ~10 from this dataset
http://www.nature.com/ng/journal/v42/n11/full/ng.680.html ), we were more
sensitive to detect duplications and deletions.

Mike


On Fri, Apr 26, 2013 at 6:24 PM, Guru Ananda <Guru.Ananda@jax.org> wrote:

>   Dear Michael,
>
>  We're interested in identifying CNVs from a single exome dataset (data
> is Illumina paired-end, and there are no controls). Reading through the
> document of your tool exomeCopy, it seemed to me that exomeCopy can
> theoretically work on a single sample, but I'm still a little unsure about
> how the background read-depth would be estimated in that case, and whether
> or not it'd be meaningful. Can you please help clarify this?
>
>  Thanks,
> Guru.
>   --
> Guru Ananda
>  Computational Sciences Group
> The Jackson Laboratory
> 600 Main St, Bar Harbor
> ME 04609, USA
> Ph: 207-288-6290
>
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