What is the best tool for extracting copy number alterations from a .maf file?  I would like to generate a .cna file which only contains inserts and deletions.  

Thanks.
You cannot do this due to the fact that the MAF [format] does not encode any copy number information specifically. Insertions and Deletions (indels) are regarded in this context as mutations, not copy number alterations. If you literally want to just extract indels from your MAF data, then that should be easy by simple `subset()` commands (in R).

There is a brief tutorial here about how one can integrate MAF data with copy number data: https://www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html

If something else, then please elaborate further on what you are aiming to do.

Kevin