Current genotyping technology is very reliable and typically produces data with both high call rates and high accuracy. However, both types of measures should be evaluated for each project because genotyping processes, reagents and instrumentation may vary. The missing call rate is a measure of data completeness, but is also a measure of genotype quality because missingness is often nonrandom. Two methods can be used to assess genotyping accuracy, duplicate sample concordance and consistency with Mendelian transmission.
