Start from SomaticSignatures R package, I am documenting the effort with cancer mutation signature.
Someone else is also interested in this and publishes signR
Since I updated NMF, now this SomaticSignatures function breaks
Popular WES analysis protocols
GeneStack hits the top on the list, way to go! The most popular free tool goes to the bedtools with an example and tutorial example by QuinLab More users' examples are available at the main bedtools manual
Nicola Roberts has a Hierarchical Dirichlet Process to extract cancer mutation signature.
License-based bioinformatics software
