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Background  Trio studies, which involve the testing of samples from a proband and both parents, are often used by clinical laboratories to help with the classification of genetic variants, including copy number variants. In order for the results of the trio study to be valid, the mother and father must be the true biological parents of the proband. As such, non-paternity and sample mix-ups are potential sources of error. To address these potential issues, we developed a computer script to accurately assess maternity and paternity using single nucleotide polymorphism (SNP) data generated by Agilent chromosomal microarrays, a platform-of-choice for clinical copy number testing.    Results  We assessed the performance of the script on 10 putative trios tested at our laboratory, and found that the numbers and proportions of discordant SNPs were useful for determining parental relationships. The results of the assessment also confirmed maternity and paternity in the 10 trios tested, and by doing so essentially excluded pre-analytical sample switching in these 30 samples.    Conclusions  Computational analysis of SNP data can be implemented as a quality control measure for trio testing performed on Agilent microarrays.    Electronic supplementary material  The online version of this article (10.1186/s12911-018-0684-9) contains supplementary material, which is available to authorized users.

Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays