gravatar for Kevin Blighe

1 hour ago by

Republic of Ireland

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: 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



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