383da828477aad2b3c6053880a64fdbfc2a00cd9 max Thu Mar 19 02:30:41 2026 -0700 Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 diff --git src/hg/makeDb/trackDb/human/sfariSparkExomes.html src/hg/makeDb/trackDb/human/sfariSparkExomes.html index e32c9ace340..606d082e50a 100644 --- src/hg/makeDb/trackDb/human/sfariSparkExomes.html +++ src/hg/makeDb/trackDb/human/sfariSparkExomes.html @@ -1,124 +1,124 @@

Description

The Simons Foundation Autism Research Initiative (SFARI) recruited a large cohort of families with autistic children who provided DNA samples and phenotypes. 54,558 families, parents and their children were sequenced, a total of 142,357 individuals with whole-exome (WES) and 12,519 with whole-genome sequencing (WGS). The data contains 32,559 trios and 8,895 quads (one sibling without autism), and 824 twins.

The same frequencies shown here are also available publicly on the SFARI Genome Browser. See (SPARK et al, Neuron 2018) for details.

Data Access

The data can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, our REST API can be used; the track name is sfariSparkExomes. For bulk download, the VCF file can be obtained from -our download server. +our download server.

Allele frequencies can also be displayed on the SFARI Genome Browser. Full CRAMs and VCFs with genotypes are available from SFARI Base. They require a data access request, which is usually reviewed quickly. More information is available in the SPARK Welcome Packet.

Methods

The genome browser track project was approved by the Simons Foundation under request number 14584.1. WES and WGS data were downloaded from SFARI Base. pVCFs were downloaded, anonymized with a script using bcftools and its "fill-tags" plugin and normalized. There was no minimum allele frequency cutoff.

The methods are documented as follows by SFARI:

WGS: This release consists of sequence and variant call data for 12,519 unique individuals, of which 12,517 (99.98%) have available genome-wide SNP genotype data. Sequencing and genotyping of all samples in this release was performed at New York Genome Center (NYGC). DNA from saliva samples were extracted and prepared with PCR-free methods and sequenced with paired-end sequencing of 150 bases on the Illumina NovaSeq 6000 system. Alignment of reads to the human reference genome version GRCh38, duplicate read marking, and Base Quality Score Recalibration (BQSR) were performed by New York Genome Center (NYGC). Whole-genome sequencing data were processed using a standardized, functionally equivalent CCDG pipeline with alignment to the GRCh38DH (1000 Genomes) reference using BWA-MEM v0.7.15 (deterministic settings, no -M, use of .alt contigs), Picard-equivalent duplicate marking (Picard ≥2.4.1 or equivalent), no indel realignment, and base quality score recalibration with GATK (dbSNP138, Mills and 1000G gold-standard indels, known indels). Final outputs were stored as lossless CRAM files with complete SAM-compliant read-group annotations and mandatory 4-bin base-quality compression (Q2—6, 10, 20, 30), and all implementations were validated for functional equivalence across centers before use. Variant Calling was performed using DeepVariant. See CCDG pipeline details.
WES: This release contains sequence data for 142,357 individuals and genotyping data for 141,368 individuals. DNA was sequenced from saliva for all samples and all participants consented to having their genetic data shared by Regeneron. Exomes for all samples were sequenced with short-read, paired-end sequencing of 150 bases on Illumina NovaSeq 6000 machines using S2/S4 flow cells. Sequencing and genotyping was performed across nine batches (WES1 through WES9) at the Regeneron Genetics Center (RGC) and integrated together for this data release. All sequencing batches were processed using the same DNA extraction methods and sequencing machines, however two different exome capture panels were used, as described below. Genotyping was performed using a SNP genotyping array for WES1 through WES4 and using "genotyping-by-sequencing" (GxS) for WES5 through WES9. The first four sequencing batches were sequenced at Regeneron using custom NEB/Kapa reagents with the IDT (Integrated DNA Technologies) xGen capture platform, including custom exome capture regions. Samples starting with batch WES5 were sequenced using the Twist Bioscience Human Comprehensive Exome panel, combined with spike-ins for sequencing genotyping sites (see Genotyping Methods), the full mitochondrial genome, and coverage boosted at selected sites for assaying clonal hematopoiesis of indeterminate potential (CHIP). SFARI performed SNV/indel calling via DeepVariant and GATK to generate gVCFs, pairwise relatedness inferred using PLINK v1.9 IBD estimates from common SNPs (AF ≥ 0.01, dbSNP v151) with ≥15% relatedness flagged, and comprehensive individual- and family-level quality control executed using the internal GenomeCheckMate pipeline to exclude samples based on contamination (≥5%), insufficient coverage (<20x in <80% of targets), sex discordance, pedigree/IBD inconsistencies, unregistered relationships, unexpected duplicates, or excess relatedness, after which QC-passing individuals (selecting the most recent passing sample per person) were retained for variant calling and joint genotyping.

-We provide documentation that indicates how all source files of the varFreqs track were converted in the makeDoc file of the track. -For some tracks, python scripts were necessary and are also available from Github. +We provide documentation that indicates how all source files of the varFreqs track were converted in the makeDoc file of the track. +For some tracks, python scripts were necessary and are also available from GitHub.

References

SPARK Consortium. Electronic address: pfeliciano@simonsfoundation.org, SPARK Consortium. SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research. Neuron. 2018 Feb 7;97(3):488-493. PMID: 29420931; PMC: PMC7444276