Pipeline for CNV calling (PennCNV-based by Wang et al., 2007 and Diskin et al, 2008). Adapted from the one developed by Auwerx et al., 2022, Lepamets et al., 2022, Mace et al., 2016, Zhang et al., 2019, Mace et al., 2017, Gao et al., 2008
This pipeline consists of a genotyping cohort originally of 576 individuals, grouped by batches (n = 12) of 48 samples each. Samples were genotyped on a Illumina array (NeuroConsortium) and gone through a QC on GenomeStudio. Remaining samples (n = 421) were exported on the form of a final report with LRR and BAF values.