To analyze compartment specific SNVs, samples were analyzed pair wise with the default settings of Strelka v0.4.7 [ref 1].  Primary tumor samples and relapse/met were compared against the germline sample. 

[ref 1] Saunders, C. T., Wong, W. S., Swamy, S., Becq, J., Murray, L. J., and Cheetham, R. K. (2012). Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28, 1811-1817.