Can anyone suggest me any software or web server to identify/screen single to few base pair alteration in cell line genome obtained from CCLE in a defined region
I assume you would need to map these mutations back to the reference human genome and then see which of them might be clustered, i.e. occurring within short distances.
I have not followed the literature, but I think these two papers show the mutations of two well-established cell lines. Is this the type of information you were looking for?
Pleasance ED, Stephens PJ, O’Meara S, McBride DJ, Meynert A, et al. (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463: 184–190. (NCI-H209 cell-line)
Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463: 191–196. (COLO-829 cell line).