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The initial steps in calling variants for diploid or multi-ploid organisms with NGS data are the same as what we've already seen:
Expectations of output are quite different however, which can add statistical power to uncovering variation in populations or organisms with more than two expected variants at the same location. If you happen to be working with a model organism with extensive external data (ESPECIALLY HUMAN), then there are even more sophisticated tools like the Broad Institute's GATK that can improve both sensitivity and specificity of your variant calls.
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