38bafc856320cf5360e0482faeee72b78f2ea963 lrnassar Tue May 5 14:13:30 2026 -0700 QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set. diff --git src/hg/makeDb/trackDb/human/sfariSparkExomes.html src/hg/makeDb/trackDb/human/sfariSparkExomes.html index 606d082e50a..a7a30e0d2d8 100644 --- src/hg/makeDb/trackDb/human/sfariSparkExomes.html +++ src/hg/makeDb/trackDb/human/sfariSparkExomes.html @@ -1,124 +1,124 @@ <h2>Description</h2> <p> The <a href="https://sparkforautism.org/" target="_blank">Simons Foundation Autism Research Initiative (SFARI)</a> 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. </p> <p> The same frequencies shown here are also available publicly on the <a href="https://genomes.sfari.org/" target="_blank">SFARI Genome Browser</a>. See (SPARK et al, Neuron 2018) for details. </p> <h2>Data Access</h2> <p> The data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. -For programmatic access, our <a href="https://api.genome.ucsc.edu">REST API</a> can be used; the +For programmatic access, our <a href="https://api.genome.ucsc.edu" target="_blank">REST API</a> can be used; the track name is <em>sfariSparkExomes</em>. For bulk download, the VCF file can be obtained from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/" target="_blank">our download server</a>. </p> <p> Allele frequencies can also be displayed on the <a href="https://genomes.sfari.org/" target="_blank">SFARI Genome Browser</a>. Full CRAMs and VCFs with genotypes are available from <a href="https://base.sfari.org/" target="_blank">SFARI Base</a>. They require a data access request, which is usually reviewed quickly. More information is available in the <a href="https://cohorts-cdn.simonsfoundation.org/spark/researcher_packets/SPARK_SFARI_Researcher_Welcome_Packet.pdf" target="_blank">SPARK Welcome Packet</a>. </p> <h2>Methods</h2> <p>The genome browser track project was approved by the Simons Foundation under request number 14584.1. WES and WGS data were downloaded from <a href="https://base.sfari.org/" target="_blank">SFARI Base</a>. pVCFs were downloaded, anonymized with a script using bcftools and its "fill-tags" plugin and normalized. There was no minimum allele frequency cutoff.</p> <p>The methods are documented as follows by SFARI:</p> <ul> <li> <b>WGS</b>: 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 <a href="https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md" target="_blank">CCDG pipeline details</a>. </li> <li> <b>WES</b>: 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. </li> </ul> <p> We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track. For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>. </p> <h2>References</h2> <p> -SPARK Consortium. Electronic address: pfeliciano@simonsfoundation.org, SPARK Consortium. +SPARK Consortium. Electronic address: <A HREF="mailto:pfeliciano@simonsfoundation.org">pfeliciano@simonsfoundation.org</A><!-- above address is pfeliciano at simonsfoundation.org -->, SPARK Consortium. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0896-6273(18)30018-7" target="_blank"> SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research</a>. <em>Neuron</em>. 2018 Feb 7;97(3):488-493. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29420931" target="_blank">29420931</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7444276/" target="_blank">PMC7444276</a> </p>