WGS targeting a mean depth of at least 30× (paired-end, 150-bp reads) using Illumina HiSeq X Ten instruments was carried out over several years at six sequencing centres (Supplementary Table 17). All sequencing used PCR-free library preparation kits purchased from KAPA Biosystems, equivalent to the protocol in the Illumina TruSeq PCR-Free Sample Preparation Guide (Illumina, FC-121-2001). Centre-specific details are available from the TOPMed website (https://www.nhlbiwgs.org/topmed-whole-genome-sequencing-project-freeze-5b-phases-1-and-2). In addition, 30× coverage WGS for 1,606 samples from four contributing studies were sequenced before the start of the TOPMed sequencing project and are included in this dataset. These were sequenced at Illumina using HiSeq 2000 or 2500 instruments, have 2 × 100-bp or 2 × 125-bp paired-end reads and sometimes used PCR amplification.
