Table 3.

Parameters and notation.

Variable	Descriptions
INPUTS TO MODEL
RT, RB	Total tumor read depth, B allele read depth
RC	Mean read depth of unmatched normals
πS, πAB, πAA	prior probability of somatic, germline heterozygous, germline homozygous variant
$Q_A^m,Q_B^m$	Mean mapping quality of reads supporting the A or B allele
$Q_B^b$	Mean base quality of bases supporting B allele
X	Total number of exons,
Y	Number of heterozygous germline variants
Z	Number of somatic variants
G	Number of segments
K	Number of clonal variant groups
J	Number of samples from the patient
ηg	Number of bases within the bed file in segment g
ηd	Number of bases within the bed file with min (F A, F B) > Fmax−somatic
PARAMETERS FIT IN MAXIMIZATION
fjk	fraction of cells in the sample j with the variants in clone k
C	centering parameter
W	controls the spread of the allelic fraction distributions
INTERMEDIATE VARIABLES
N	total copy number
M	minor allele copy number
φS, φG	expected allele fraction of somatic or germline variant
IS, Ij	Index of clonal subset containing somatic variant or copy number variant
A	Allele of somatic variant (A = 1 for allele A = 2 for minor allele)
XCNA	Number of copy number altered exons
OTHER NOTATION
GAA, GAB	Germline homozygous or heterozygous genotype
O	Other genotype beside somatic, germline homozygous AA, or germline heterozygous AB
U	Unknown genotype due to poor mapping
k	Index of clonal subset {1, 2, …, K}
g	Index of segment {1, 2, …, G}
z	Index of somatic variant {1, 2, …, Z}
y	Index of heterozygous variant {1, 2, …, Y}
x	Index of exon {1, 2, …, X}