NGS-variants-training/2022.9/day2/variant_calling/

[giscus[bot]]

NGS-variants-training/2022.9/day2/variant_calling/

https://sib-swiss.github.io/NGS-variants-training/2022.9/day2/variant_calling/

[GeertvanGeest]

To run the R code, here's an example for calculating the PL of the homozygous reference:

genotype_likelihood <- function(m,g,e,ref,alt){
  (((m-g)*e+g*(1-e))^alt * ((m-g)*(1-e)+g*e)^ref)/(m^(ref+alt))
}

likelihood <- genotype_likelihood(  m = 2, 
                                    g = 0, 
                                    e = 0.01, 
                                    ref = 22, 
                                    alt = 4)
-10*log10(likelihood)