When applying for a position, how do I best reply to a question asking for skills I don’t have?
First of all, do not worry too much about whether this is a strict requirement for the position.
This is something they have to decide (based on your honest assessment of your prerequisites).
Also, if you made it past the first stage of the hiring process, it is likely that this is not a strict criterion.

Additionally note that (depending on country, field, and individuals) job ads that ask for more than they can possibly get are sadly common and in this case it is no problem if you only have a subset of the skills they ask for.
Whether this actually applies to your situation is something you have to judge yourself:
How likely is it that somebody already acquired all the mentioned skills at your stage?
In particular if we are talking about a PhD position here, acquiring relevant skills on the job should be the norm.

That being said, when faced with such a question:


Answer truthfully. You don’t want to do a job you cannot do and it almost certainly ruins your relationship with your advisor if they suspect you were dishonest about this.
Is there anything similar you have experience with or anything that may facilitate you learning these skills? If yes, talk briefly about this.
Do you find the methods in question interesting? If yes, state so and explain why. (If no, you probably should look for another position.) It may very well be that you were asked this question just to check that you do not shiver with disgust in light of these methods.
If it wouldn’t be uncommon to have these skills at your level, explain why you do not have them. For example, if your past universities did not offer a course on them, state this.