I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html

Specifically, the .bam files. I would like to find alignments for neanderthal sequences to human genomes that state ambiguities (such as M or R). However, the data from that site does not have the ambiguities. Is there a way to find such information? Or are there no ambiguity codes in neanderthal alignments?

My goal is to compare diploid neanderthal sequences to diploid human sequences. How do researchers typically deal with this given the limited data they have for neanderthals?