Example datasets for use with CNVkit, derived from sequencing data from these published studies:
Targeted & exome (desmoplastic melanoma):
Shain, A.H., Garrido, M., Botton, T., Talevich, E., Yeh, I., Sanborn, J. Z., Chung, J., Wang, N.J., Kakavand, H. Mann, G.J., Thompson, J.F., Wiesner, T., Roy, R., Olshen, A.B., Gagnon, A., Gray, J.W., Huh, N., Hur, J.S., Busam, K.J., Scolyer, R.A., Cho, R.J., Murali, R., Bastian, B.C. (2015). Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nature Genetics. doi:10.1038/ng.3382
Cell line (C0902):
Botton, T., Yeh, I., Nelson, T., Vemula, S.S., Sparatta, A., Garrido, M.C., Allegra, M., Rocchi, S., Bahadoran, P., Mccalmont, T.H., Leboit, P.E., Burton, E.A., Bollag, G., Ballotti, R., Bastian, B.C. (2013). Recurrent BRAF kinase fusions in melanocytic tumors offer an opportunity for targeted therapy. Pigment Cell and Melanoma Research, 26, 845-851. doi:10.1111/pcmr.12148
See also the CNVkit preprint manuscript.