Are you looking for genotyping or sequencing methods for ancient human DNA or would you like information on the analysis of the haplotypes/genotypes/sequences that you would obtain? What is the number of subjects and the material at your disposal?

Studying ancient DNA is the same as studying modern DNA, except for the degraded state of most samples, which means you can obtain Y-chromosome haplotypes (STR and/or SNP), mitochondrial haplotypes (mostly SNP, short sequences or complete mtDNA), autosomal genotypes (STR or SNP) or complete (or partial) nuclear genome sequences (including the Y-chromosome).

Analysis methods will depend on the objective of your studies. Population genetics in general, pedigree testing, phenotype analysis, forensic identification methods all work on ancient human DNA.

If you can specify I would be glad to try to help.

Hi, 

if you are looking to a general overview about the lab methods to extract ancient DNA you can start with the book http://www.springer.com/us/book/9781617795152. After reading it you will need to get some updates on specific methods, because it was written in 2012. 

About the analysis of data my colleagues and me have been discussing the topic of ancient DNA data analyses in a recent review paper that you can find attached to this reply. 

The mentioned references are very general, so if you can better specify what you are looking for I can provide additional references.

Best

Article Evolutionary Patterns and Processes: Lessons from Ancient DNA

Thanks for replying and I'm really sorry about the late reply!