Detection of de novo copy number deletions from targeted sequencing of trios.

Motivation: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms.

Results: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in amuch higher positive predictive value (precision). MDTS also exhibitedmuch better scalability.

Availability: MDTS is freely available as open source software from the Bioconductor repository.

Supplementary information: Supplementary data are available at Bioinformatics online.