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I am interested in software engineering specifically software testing and program analysis.

Do I need to use a comma before or after specifically in the above sentence?

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    Before, to prevent your reader from parsing your sentence as meaning that your interest is specifically in software engineering. – deadrat Aug 22 '16 at 2:16
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This is a punctuation/typesetting issue, so there will be several potential solutions. As the writer, how do you want your readers to interpret the sentence and how do you want them to flow with the sentences around it? Where do want the pause? What you don't want are your readers needing to re-read because of ambiguity.

Because you don't have two complete sentences connected by an adverb, your grammar is fine either way. Taking into account Rat's comment, I'd write this

I am interested in software engineering--[m-dash] specifically, software testing and program analysis.

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