Fig. 2
From: Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
Schmutzi workflow. An initial contamination estimate is computed using the deamination rates of fragments by conditioning on the other end being deaminated and comparing these to the deamination rate of all fragments in the dataset (contDeam). This prior is provided to call an endogenous consensus (endoCaller). The consensus call is, in turn, used to re-estimate mitochondrial contamination (mtCont). Deamination rates and fragment length distributions are measured for fragments that support endogenous and contaminant mitochondrial genomes (splitEndo). The information from mtCont and splitEndo is used as input for re-calling the endogenous consensus (endoCaller). This cycle is repeated until a stable contamination rate is reached. db database