- 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.