Schizophrenia risk conferred by rare protein-truncating variants is conserved across diverse human populations
Ion AmpliSeq technology is an amplicon-based enrichment method for creating sequencing libraries. We used Ion AmpliSeq Designer version 6.13 to design amplicons that cover the exons of the 161 genes defined based on the Ion hg19 reference. Mean and median percentage of covered base pairs across all exons were 97.7% and 100%. Sequencing of the PGC3SEQ samples was performed on the Ion Torrent platform at Sema4 in between June 2018 and April 2019. Sequencing plates were matched with respect to ancestry and case-control composition whenever possible. The average sequencing depth across all samples was 224×. Sema4 sequencing facility returned to the research team BAM files with flow signal and associated QC metrics. Single sample calling was performed using Torrent Variant Caller v5.8.0, which is specially optimized to exploit the underlying flow signal information generated by the Ion Torrent sequencing. Sites were left-aligned, normalized, and multiallelic sites were split into separate lines using BCFtools v.1.9.