A total of 2,174 whole genomes have been available since August 2016, including most of the samples from the Pilot study and Phase 1 (see Table 1). For these data, alignment of reads to hg19/ National Center for Biotechnology Information (NCBI) build 37 was done using Burrows-Wheeler Aligner (BWA) software package (BWA-MEM), and all local realignment and variant calling was done using Genome Analysis Toolkit (GATK) best practices (version 3.4). These data have now been reprocessed using a different computational pipeline, which uses BWA-MEM (0.7.15) alignment of reads to hg38/NCBI build 38, with adjustments to sorting of duplicate markings and base quality score recalibration. Variant calling was done using GATK (version 3.5).
In addition to this reprocessed dataset, we are also releasing BAM (Binary Alignment/Map), CRAM (compressed versions of the alignment) and VCF (variant call format) files for an additional 6,801 whole genomes (i.e., 1,369 quad families [5,476 genomes], 437 trio families [1,311 genomes] and 14 genomes from partial families). Structural variant calls are being processed and will be made available as soon as possible. These new genomes were sequenced in batches and were processed using the same computational pipeline employed for the reprocessing of the Pilot study and Phase 1 data, as described above. The sequencing batches and publication embargoes (if applicable) are outlined in Table 1.
Note: Most of the data detailed in Table 1 are currently available, although some datasets are still in transit from the New York Genome Center (NYGC) and will be available in the coming weeks. Furthermore, there are an additional 86 probands with incomplete families that will be released in the near future.
