Is CopySeq suitable for exome sequencing data?

[DONGHAI XIONG]

Dear Author:

It is nice to see your wonderful program of CopySeq which should be
able to predict copy number status accurately. However, I am mainly
dealing with large sets of whole exome sequencing data.

So I want to know eagerly whether CopySeq can infer CNVs from exome
sequence data accurately as well? What are the best setting of
parameters?

Thanks a lot!

[Sebastian Waszak]

Dear Donghai,

Unfortunately, CopySeq is currently not designed to run on exome
sequence data. The main reason for this is that the model parameter
estimation for the G+C bias and the read-depth variance estimation is
dependent on loci which are scattered all around the genome. At the
moment I am not planing to further develop CopySeq for exome
sequencing data since I am not working with this type of dataset.
Please have a look at one of these tools which might work on your
datasets:

http://seqanswers.com/wiki/Special:BrowseData/Bioinformatics_application?Biological_domain=Copy_number_estimation

Best wishes,
Sebastian