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Table 1 Inputs and outputs for the different programs described in ‘Methods’. Overview of the three main programs, contDeam, endoCaller and mtCont, with the helper program splitEndo for the iterative mode

From: Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA

Program

Input

Output

contDeam

BF

CRDP, EDR

endoCaller

BF, EDR, CP, DFL

EB

mtCont

BF, EDR, DB, EB

CRDB, CS

splitEndo

BF, EB

EDR, DFL

  1. BF BAM file, CRDP present-day human contamination rate using deamination patterns, CRDB present-day human contamination rate using a database of putative contaminants and the endogenous base, EDR endogenous deamination rates, CP contamination prior, DFL distribution of endogenous/contaminant fragment lengths, EB endogenous base, DB database of putative mitochondrial contaminant genomes, CS most likely contamination source
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Genome Biology

ISSN: 1474-760X

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