I am currently taking a Bachelor of Computing Science specializing in Bioinformatics and debating whether I should get a masters or not. How pivotal is getting a masters? What are the pros and cons? One step further if you think the masters is required what is your take on taking a PHD?
This is a very large issue, and your question is incompletely stated. Your question can't really be answered in a concise way. My opinion is the proper way to frame this question would include detail about:
What kind of work environment do you want to live in? It is difficult though not impossible to get a position in an academic lab with a Masters degree. You will have a serious ceiling on some kinds of career progression, but the trade-offs may be worthwhile. (Note: this point is a long discussion topic).
How many years can you afford to spend on education? Remember that even life in a PhD program where you receive a stipend has an opportunity cost, since you would most likely get paid more even as a Research Assistant. The median length of a PhD is about 6 years.
How much money can you spend? Many masters programs are not paid for unless you get a research assistantship. Private programs are very expensive.
Do you know what you're getting yourself into? Many Masters programs are not that different from college. PhD programs are not like college, although it might seem that way for the first year.
What kind of position are you targeting? If the answer is "tenured professor", then your choice is a PhD, although that's just the start of the road. If the answer is "I want a staff position working in a bioinformatics core or lab in an academic institution" then you may be able to get by with a masters degree.
What kind of degree program would you consider? There are many different programs out there. Some are an appendage of the computer science department and don't contain working wet lab biologists. Some are independent. Some require you to write a thesis (which is a good thing).
I recommend browsing the forum on the Science magazine careers site as this exact question has been asked several times there.
The most important skill is the one gained from solving real bioinformatics problems. Find someone who needs computational solutions (pretty much all biologist need that!) and help them.
Some time ago I have interviewed several candidates and the ones that stood out by far were those who worked on realistic problems rather than just in-class examples/homeworks. The degree on its own is not all that telling.
Like others have already said, the answer to your question depends very much on what you would like to do in the future. If you want to become a researcher in academia, there is pretty much no way around doing a PhD. If you want to be a researcher in industry, it will also be hard without a PhD at at least a masters.
One perspective that I would like to add is the option to do a PhD abroad after having done a masters. Most European countries require you to have a masters before you can start on a PhD, however, because you start with more experience it only takes 3-4 years to do the PhD. One big advantage is that in some countries - for example, Denmark where I live - the salary of a PhD students is comparable to what you could expect to get elsewhere having just finished a masters. In other words, the opportunity cost of doing a PhD is minimal in this case.
Also, I would strongly recommend that if you do a masters, you use it as an opportunity to broaden your knowledge. To be successful in bioinformatics, you need to have a good working knowledge about computer science as well as biology. I do not know how the system works where you are, but if it is possible to do a masters that is focused on (molecular) biology on top of a bachelor in computer science, that would give you a very strong background. Being in the process of starting up my own research group, I can tell you that people with good computer skills and biological knowledge are rare and much sought after.
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You mentioned that getting a masters focused on molecular biology is a big plus. Currently in my bioinformatics program I can choose something similiar to "concentration" on either Genetics or Molecular Biology. Which one would you advice to take?
In my opinion either would be a good background - what matters in my opinion is that it is in the biology end of the spectrum rather than the computer science end. Which exact subfield you should choose really comes down to personal preference; chances are that in the end you won't be working on the exact thing you studied anyway ;-)