Skip to main content

Table 3 Description of priors used in Seurat

From: Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs

Symbol

Description

Default values

πι

Genotype prior probabilities

πvar = 0.0005

πhet = 0.001

πref = 1 – (πhet + πvar) = 0.9985

Ï€somatic = 0.0001

Ï€LOH = 0.0001

αι, βι

Alpha and beta hyperparameters for the beta distributions of variant allele proportions

αref = 1, βref = 700

αvar = 700, βvar = 1

αnonhom = 1, βnonhom = 1

αsomatic = 1, βsomatic = 1

αAI = 1, βAI = 1

  1. Detailed Legend: A list of the priors and hyperparameters used by Seurat, and their assigned values. The priors used for the genotype in the normal genome are the SNP frequencies for human diploid chromosomes, as calculated by Li et al. [24]. πsomatic and πLOH are high-end estimates of the frequency of somatic events, given that that the mutation profile of each individual cancer can vary wildly even within subtypes. At 0.0001, they expect 300,000 events through the human genome.