Version: Chirmade 2025 release Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
This track shows small-variant (single-nucleotide variant and short-indel)
allele frequencies from 101 samples released as part of the
GWAS
SVatalog tool (Chirmade et al. 2026). The same 101-sample cohort
underlies the structural-variant sibling track
SVatalog 101 SVs in the Long-read
SV collection; this track provides the companion small-variant allele
frequencies that SVatalog uses to compute linkage disequilibrium between
SNPs and SVs.
The callset contains about 8.8 million sites across the autosomes
and chromosome X. Each site reports the alternate allele frequency in the
101 samples, the gnomAD v3.1 non-Finnish European allele frequency (when
annotated in the source release), and a dbSNP rsID when one was available.
Display Conventions and Configuration
The track uses the standard VCF display. Variants appear as colored marks
along the genome; clicking an item opens the detail page with per-site
INFO fields: AF, AC, AN, the gnomAD v3.1 NFE allele frequency
(GNOMAD_NFE_AF) and the dbSNP rsID (RSID).
Note on AC/AN: the source allele-frequency release only ships AF. For this
track we synthesize AC and AN by assuming the full 2x101 = 202-allele
denominator (AN=202, AC=round(AF x 202)), so the values are approximate
at sites where some samples had missing genotypes.
Methods
Small variants were called from 10X Genomics linked-read (paired-end
short-read) whole-genome sequencing of the 101 SVatalog samples with
GATK
HaplotypeCaller v4.0.0.0 using default parameters. Calls were phased
across the cohort with
SHAPEIT
v4.2.0, and per-site alternate allele frequencies were computed on
the resulting joint callset. Structural variants, released as a separate
lrSv subtrack, were called from long-read data and merged with these
SNPs for the LD analyses reported by GWAS SVatalog.
For display here, the per-chromosome allele-frequency text files
(chr{1..22,X}_allele_freq.txt) were converted to a single
sites-only VCF with approximate AC/AN fields and bgzipped / tabix
indexed. The step-by-step build commands are recorded in the UCSC
makeDoc
doc/hg38/varFreqs.txt; the converter script lives in
makeDb/scripts/varFreqs.
Data Access
The VCF file for this track is available from
our
download server as svatalog.vcf.gz (with .tbi index).
Regions can be extracted with tabix:
tabix http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/svatalog/svatalog.vcf.gz chr21:1-100000000.
The original per-chromosome allele-frequency tables and the accompanying
LD statistics used by the SVatalog tool are available from the
companion Zenodo deposit:
zenodo.org/records/13367574.
The SVatalog web tool itself is at
svatalog.research.sickkids.ca.
Credits
Thanks to Chirmade, Strug and colleagues at The Hospital for Sick
Children and the University of Toronto for releasing this annotated
SNP frequency callset alongside the GWAS SVatalog tool.