– Number of variants
– Transition/transversion ratio
– Hardy-Weinberg Equilibrium violations
- Presence in variant databases
– % in dbSNP build
– Concordance to Hapmap (II, II+III consensus, III)
– Concordance to validation data (i.e. array-based genotyping)
- Visualization (IGV*)
– Examination of alignments, local sequence context, error covariates, etc.
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