Table 3 Other model parameters and variables

 R_T, R_B

Total read depth, B allele read depth

 π_S, π_AB, π_AA

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

 f_i

fraction of cells in the sample with the variants in clone i

 C

centering parameter

 W

controls the spread of the allelic fraction distributions

 N

total copy number

 M

minor allele copy number

 ϕ^S, ϕ^G

expected allele fraction of somatic or germline variant

 I_S, I_j

Index of clonal subset containing somatic variant or copy number variant

 Q^*

Number of copy number altered exons

 G_AA, G_AB

Germline homozygous or heterozygous genotype

 O

Other genotype beside somatic, germline homozygous AA, or germline heterozygous AB

 U

Unknown genotype due to poor mapping

 i

Index of clonal subset {1, 2, ..., K}

 j

Index of segment {1, 2, …, G}

 s

Index of somatic variant {1, 2, …, Z}

 h

Index of heterozygous variant {1, 2, …, Y}

 n

Index of exon {1, 2, …, X}