Hello everyone! Usually, there are two lines drawn at the manhattan plot: suggestive and genome-wide significance lines. It is clear that the genome-wide significance line corresponds to Bonferonni-corrected p-value namely 0.05 divided by the number of SNPs tested. The suggestive line lies a little bit lower than genome-wide significance lines and serves as a more soft threshold. The googling on how the suggestive line is calculated led me to no success. If you know paper explaining it or a FAQ/tutorial please recommend.
1 answer
That line is kinda selected arbitrarily. As the genome wide significant threshold is 5e-8, a "suggestive" line of 5e-7 is usually used because it is one level up. Though in most case, the suggestive line isn't that useful and are sometime use to make the exaggerate the finding of the study
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