computeAFMutMatrix

Calculate the allele frequency per variant. Source: https://github.com/petervangalen/MAESTER-2021 We can get AF values greater than 1, which is due to uninformative reads. See: https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD-is-lower-than-expected and https://github.com/caleblareau/mgatk/issues/1 We simply set these values to 1, since that is the actual information we have in this case.

Usage

computeAFMutMatrix(SE, chromosome_prefix = "chrM")

Arguments

SE

SummarizedExperiment object.

chromosome_prefix

The prefix of the chromosome.