We assembled approximately 1 petabyte of raw sequencing data (FASTQ files) from 91,796 individual exomes drawn from a wide range of primarily disease-focused consortia (Supplementary Information Table 2). We processed these exomes through a single informatic pipeline and performed joint variant calling of single nucleotide variants (SNVs) and short insertions and deletions (indels) across all samples using a new version of the Genome Analysis Toolkit (GATK) HaplotypeCaller pipeline. Variant discovery was performed within a defined exome region that includes Gencode v19 coding regions and flanking 50 bases. At each site, sequence information from all individuals was used to assess the evidence for the presence of a variant in each individual. Full details of data processing, variant calling and resources are described in the Supplementary Information Sections 1.1–1.4.
