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 |

F_{max-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 |