Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files

Question

[James G]

Hi,

Does anyone know if there's an existing tool to calculate genetic distances between query and subject sequences in BAMs/SAMs? I'm reasonably sure it's possible to identify transitions and transversions using data from the MD flag and the sequence, and from that calculate genetic distance, however I don't know if I'll need to write my own tool or if one already exists.

Cheers, James.