Tools to deal with aDNA damage

less than 1 minute read


  • mapDamage –rescale option changes quality scores on bam files
  • PMDtools - filters out contaminant reads based on deamination profiles AND adjust scores too. Works on SAM files.
  • ATLAS toolset can do BQSR
  • AntCaller - genotype caller for ancient genomes. Works better than GATK according to the paper.
  • SpAl - estimate the proportion of spurious alignments in ancient DNA. Works with any species, as long as there is data on variation in the genome.