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Cost
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Lower cost
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Higher cost
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Genomic coverage
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Best for variants for which DNAs of all genotype combinations are available, i.e., not robust for rare variants
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Appropriate for detection of nearly all genetic variation in the genome depending on the depth of sequencing, i.e., not robust for difficult to sequence regions
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Requires prior knowledge of the variant, i.e., unable to detect private variants not previously reported
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Reduced accuracy in genomic regions of low complexity
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Reduced accuracy in genomic regions of low complexity
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Analyses
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Well established analytical protocols and tools for data analyses
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High computational costs and greater analytical complexity
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Larger multiple testing burden when conducting single-variant tests
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Greater costs to store, process, analyze and interpret the resulting data
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Suitability
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Screening
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Diagnostic testing
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Analyzing known or candidate associations in large cohorts
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Detecting and fine-mapping rare variants
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Detecting low-frequency, common variant associations in large sample sizes
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Detecting ultra-rare risk variants when it becomes economically viable to perform WGS at a very large scale
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