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 |