Fig. 1

Rare CNVs workflow. The pipeline consists of two major sub-pipelines: (1) Calling and quality control (QC) analysis, which uses the SNP-array genotyping data (green box) as an input to retain good-quality samples and high-quality calls. (2) Rare CNV analysis, which takes samples and calls from the calling and QC sub-pipeline output, and after the data format conversion, performs the burden, rare CNV and enrichment analyses. Black dotted lines split each analysis in their corresponding modules, purple boxes represent a specific task in each module, yellow boxes show representative outputs (files and/or plots), yellow line box represents an external dependency, and the blue box represents external functions used by some modules. Dotted purple boxes are optional tasks which could be easily removed or changed to adapt the pipeline to the study requirements