The SPARK WGS August 2026 release (SFARI Base dataset DS0000135) adds whole genomes for 45,178 individuals from 21,003 families, 20,858 of them with autism. This is a mostly new set of people: only 14 of them are also in the 12,519-genome release and 201 in the exome release. It includes about 4,900 trios with an autistic child and 1,800 quads. The genomes were sequenced PCR-free on the Illumina NovaSeq X at Broad Clinical Labs. The track "SFARI SPARK 45k WGS ASD" shows this release. Its counts were computed from the genotypes, with the autism/non-autism split and all variants, including those seen only once. Millions of long insertions in this release are bacterial DNA from the saliva samples, not human variants. They are marked and hidden by -default (see Methods). +default (see Methods). SFARI has told us that the alignment step of this release did not +handle the alternate haplotype sequences of GRCh38 correctly. They plan to realign the reads +and call the variants again, and this track will be updated when the new data is available.
The same frequencies shown here are also available publicly on the SFARI Genome Browser. See (SPARK et al, Neuron 2018) for details.
In addition to the overall allele count (AC), allele number (AN), and allele frequency (AF), each variant record carries counts split by autism status (the asd column of the SPARK individual registration file):