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Tiger / truthSetErrors

Overview

Assess how many calls of the true sample are actually incorrect

  1. Fill 3x3 frequency table [t][r] reflecting the frequency with which a true call t is reported as call r based on sequencing errors, integrating over all possible number of true alternative alleles
  2. Use the probability of a heterozygous genotype to create a 3x3 counts table from the frequency table
  3. From the counts estimate the per allele genotyping error rates as describes in Bresadola et al. (2018)

Parameters

  • error: If errorHet is given, this is the error rate assumed for homozygous sites. If not, this is the overall error rate
  • errorHet: the error rate assumed for heterozygous sites
  • het: default = 0.1
  • seqError: default = 0.01
  • maxDepth: default = 30

Updated