I got a rather unusual question and would appreciate suggestions or discussion. Let say one has a good set of high quality sequencing reads, purportedly for bigfoot or sasquatch, which is likely a great ape, but no more is known than it is likely closer to Homo than to other great apes. But may be not. If a goal is to do some population genetics studies with this data set, one needs to assemble its genome and get as much variant calling as possible, and then run those comparisons. De novo assembly is not likely an option (is it?), so what are options for reference assembly? If using the human genome as a reference, there is a danger of loosing a lot of crucial variants and getting quite skewed results. If using the chimp or gorilla genomes for reference assembly, then how to proceed after that with variant calling and comparison with human variations? How would you approach this?
I don't have an answer to your questions.
Two suggestions: 1) Try to use a more informative title. As it is, this topic could literally be about anything, and only curious people will open it. Since not everyone who is curious will also know the answer - I would be in that group - it would likely help you to edit your title into something more informative that will attract knowledgeable people; 2) It would help the discussion if you show your thinking and ideas about this problem. As it is stated, it appears to be a homework that you want someone else to solve for you.
Perhaps you are right, but the intention was mainly to at least get suggestions where to start doing my homework on searching for a suitable approach. Would bigfoot in the title attract more attention? I doubt given the controversial nature of the topic and known failures of purported bigfoot genetic studies. If you think you can help in attracting attention of knowledgeable people to discussion on the topic I would appreciate your advice.