4.10 PMDS
Filtering for ancient reads using PMDS (Post mortem damage score)
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. One way of measuring contamination or filtering out reads that most likely originate from modern DNA is to use the post-mortem damage score (PMDS) introduced by Skoglund et al. (2014). With this task, you can use ATLAS to calculate the PMDS for all reads. The output is a new BAM file, where each alignment is described by a field DS:f:<PMDS>, which specifies the alignment’s PMDS score. If the DS field already exists, it will be overwritten. It is possible to filter out the reads with a low PMDS score while writing the BAM file by using the option minPMDS or maxPMDS to specify the threshold value.
A PMDS score > 0 means that the read is more likely ancient than modern. The higher the score, the higher its probability of being ancient.
4.10.1 Parameters
4.10.1.1 Input
--bam Input_bam_file.bam |
Input bam file |
--fasta Input_refrence_genome_file.fasta |
Reference genome |
4.10.3 Usage Example
# Simulate a BAM File with exponential pmd pattern
atlas simulate --pmd "CT5:0.2*exp(-0.3*p)+0.07;GA3:0.2*exp(-0.25*p)+0.06"
# estimate PMD pattern
atlas estimateErrors --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta --out ee
# Create BAM file with PMDS scores using PMD pattern in 'ee_RGInfo.json'
atlas PMDS --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta --RGInfo ee_RGInfo.json
# filter file with PMDS score > 1
atlas filterBAM --filterPMDS ,1 --bam ATLAS_simulations_PMDS.bam