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 a much higher positive predictive value (precision). MDTS also exhibited much better scalability. AVAILABILITY AND IMPLEMENTATION: MDTS is freely available as open source software from the Bioconductor repository. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.