What are the differences between the two methods?
What advantages does one have over the other, and what are their limitations relative to one another?
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4$\begingroup$ This question is too broad, and is prone to subjective answers that aren't very helpful. Please try to narrow your question, preferably thinking about a specific task that you would like to carry out. $\endgroup$– gringer ♦Dec 9, 2017 at 19:46
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1 Answer
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Most papers that I've looked at distinguish between looking for genotype/trait associations in mapping populations created by experimental crosses (QTL mapping) and looking for genotype/trait associations in populations of unrelated individuals (GWAS). No distinction is made between susceptibility to disease (often referred to as a case-control GWAS) and continuous traits (all of the big studies on genetic associations with height use the term GWAS, for example).
Many of the papers in my first link use both methods, so you can take a look at them to get an idea of the advantages and limitations of each.
