I have been doing some ancient DNA bioinformatics for a while now and have been using the bwa aln command.
When using this command with ancient DNA it is recommended to disable seeding. This slows down alignments somewhat but allows the damaged DNA sequences to be aligned, the characteristic damage is a C->T transition at the 3' end of the sequenced fragments. For instance I use the parameters -l 1024 (to disable seeding) -o 2 (increase gap open slightly) and -n 0.03 (reduce the edit distance slightly). These parameters were taken from this paper
Are there any specific settings required to use bwa mem with ancient DNA?
Does bwa mem use seeding at all?
Thanks in advance