Table 2.

Parameters and default values.

Parameter	Default value or source	Description
f π	0.1,0.7	Vector of length J of initial sample fractions. Default assumes two samples, with low and high tumor content.
απ	1.5	Determines shape of prior distribution of Δf
π (N = 0) …π (N = 3), π (N ≥ 5)	0.01,0.25,0.3,0.2,0.15,0.09	Copy Number Priors
π (M = 0), π (M = 1), π (M ≥ 2)	0.25,0.5,0.25	Minor Allele Copy Number Priors
αseg	1E-5	Segmentation significance cutoff
ω	COSMIC	Number of cancer variants observed at the position
FA, FB	1,000 Genomes and Exac	Population Allele Frequencies
ρSNV, ρindel	1E-5, 1E-6	Constant for calculating prior somatic
Fp−SNV, Fp−indel	1E-5, 1E-6	Population allele frequencies assigned to alleles not seen in input population
Fmax−somatic	2E-5	Maximum population allele frequency to be considered a possible somatic variant
$Q_{min}^m$	10	Minimum mapping quality to count read
$Q_{min}^b$	5	Minimum base quality to count base
T PASS	0.8	Minimum posterior probability of belonging to the PASS group to be called pass
T Somatic	0.8	Minimum posterior probability of variant is somatic to be called somatic
T Germline	0.8	Minimum posterior probability of variant is germline to be called germline
ξ	3	Number of parameter fitting iterations without new global minimum before stopping
λ	5	Weight of penalty for adding clonal variant group