Version: Cohen 2022 release Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
This track shows small variants (single-nucleotide variants and short
insertion/deletion variants) identified by PacBio HiFi long-read sequencing
of probands and their families enrolled in the Genomic Answers for Kids
(GA4K) program at Children's Mercy Research Institute. GA4K is a longitudinal
pediatric genomics initiative that aims to enroll 30,000 children with
suspected rare genetic disorders, together with their parents, to build a
large-scale resource of clinical and genomic data.
The callset contains approximately 36.2 million variants genotyped across
up to 552 samples (maximum allele number 1104 on the autosomes). Each
variant is annotated with allele count (AC), total called alleles (AN),
cohort allele frequency (AF), variant type (substitution, insertion or
deletion), and the corresponding gnomAD v3.0 allele frequency if one is
available.
Display Conventions and Configuration
The track uses the standard VCF display. By default, variants appear as
colored marks along the genome. Click an item to open its detail page,
which lists the per-site INFO fields AC, AN, AF and the gnomAD v3 allele
frequency.
Methods
Samples were sequenced on PacBio Revio and Sequel II instruments with HiFi
chemistry. Per-sample variant calls were generated with DeepVariant as gVCFs,
then merged across the cohort with GLnexus v1.2.7 using the
DeepVariant_unfiltered configuration. The resulting BCF was converted
to VCF with bcftools view v1.10.
To reduce false positives, the merged callset was filtered to variants
replicated by independent evidence: (1) observed in at least one additional
unrelated Children's Mercy individual, or (2) matching a variant observed in
a sample from the Human Pangenome Reference Consortium (HPRC).
The GA4K release ships as 24 per-chromosome VCF files (chr1-22, chrX,
chrY). For the Genome Browser, these were concatenated with
bcftools concat into a single bgzip-compressed, tabix-indexed file.
Data Access
The VCF file for this track is available from
our
download server as ga4kSnv.vcf.gz (with .tbi index).
Regions can be extracted with tabix, for example:
tabix http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/ga4k/ga4kSnv.vcf.gz chr21:1-100000000.
The original per-chromosome VCFs and full release documentation are
available from the Children's Mercy Research Institute GA4K data release at
github.com/ChildrensMercyResearchInstitute/GA4K.
Credits
Thanks to the Children's Mercy Research Institute and the Genomic Answers
for Kids participants and their families, who released this dataset to the
public.