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Table 3 Other model parameters and variables

From: A method to reduce ancestry related germline false positives in tumor only somatic variant calling

Variable Descriptions
Inputs to model
 RT, RB Total read depth, B allele read depth
 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
Parameters fit in maximization
 fi fraction of cells in the sample with the variants in clone i
 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
 Q* 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
 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}
  1. Key to notation used in describing model