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