Table 2.

Model input parameters

Parameter	Default value or source	Description
K	3	Number of Clones
f π	0.5	Mode of prior distribution of f
α π	1.5	Determines shape of prior distribution of f
π(N = 0)…π(N = 3), π(N ≥ 4)	0.1, 0.15, 0.5, 0.15, 0.1	Copy Number Priors
π(M = 0), π(M = 1), π(M ≥ 2)	[0.25;0.5;0.25]	Minor Allele Copy Number Priors
α seg	1E-5	Segmentation significance cutoff
ω	COSMIC	Number of cancer variants observed at the position
F A, F B	1000 Genomes	Population Allele Frequencies
ρ SNV, ρ indel	1E-5, 1E-6	Constant for calculating prior somatic
F p − SNV, F p − indel	7.14E-5, 1.43E-5	Population allele frequencies assigned to alleles not seen in input population
Fmax-somatic	1E-3	Maximum population allele frequency to be considered a possible somatic variant
$Q_{\mathit{min}}^m$	10	Minimum mapping quality to count read
$Q_{\mathit{min}}^b$	5	Minimum base quality to count base
ΤPASS	0.99	Minimum posterior probability of belonging to the PASS group to be called pass
ΤSomatic	0.8	Minimum posterior probability of variant is somatic to be called somatic
ΤGermline	0.8	Minimum posterior probability of variant is germline to be called somatic

Where applicable, default values were determined empirically on an independent data set