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Table 2 Model input parameters

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

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
\( {Q}_{min}^m \) 10 Minimum mapping quality to count read
\( {Q}_{min}^b \) 5 Minimum base quality to count base
Τ PASS 0.99 Minimum posterior probability of belonging to the PASS group to be called pass
Τ Somatic 0.8 Minimum posterior probability of variant is somatic to be called somatic
Τ Germline 0.8 Minimum posterior probability of variant is germline to be called somatic
  1. Where applicable, default values were determined empirically on an independent data set