Overview

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.

Input

• BAM file
• FASTA reference
• pmdFile (see Diagnostics: estimatePMD for producing such a file)
• Base quality score recalibration files (see BQSR or recal for producing such files)

Output

• A BAM file (filtered or not), where each alignment has a tag DS:f:<PMDS> recal=example_recal.txt

Usage Example

./atlas task=PMDS bam=example.bam pmdFile=example_PMD_input_Empiric.txt recal=example_recalibrationEM.txt verbose

Specific Arguments

• minPMDS : filter out reads that have a PMDS score below the specified value. Default = -10000
• maxPMDS : filter out reads that have a PMDS score above the specified value. Default = 10000

Engine Parameters

Engine parameters that are common to all tasks can be found here.