9bfd58221b1539193cb7f0a317b4e959c1c7e49a
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Thu May 21 01:00:45 2026 -0700
varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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index 2f00876c279..db1dd921b1d 100644
--- src/hg/makeDb/trackDb/human/ga4kSnv.html
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@@ -1,81 +1,81 @@
<h2>Description</h2>
<p>
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.
</p>
<p>
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 allele frequency in gnomAD v3.0 where
+deletion), and the corresponding gnomAD v3.0 allele frequency if one is
available.
</p>
<h2>Display Conventions and Configuration</h2>
<p>
-The track uses the standard VCF display. By default, variants are shown as
-colored marks along the genome; clicking an item opens the detail page
-with per-site INFO fields including AC, AN, AF and the gnomAD v3 allele
+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.
</p>
<h2>Methods</h2>
<p>
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
<tt>DeepVariant_unfiltered</tt> configuration. The resulting BCF was converted
to VCF with <tt>bcftools view</tt> v1.10.
</p>
<p>
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).
</p>
<p>
-The GA4K release is provided as 24 per-chromosome VCF files (chr1-22, chrX,
-chrY). For display on the Genome Browser, these were concatenated with
+The GA4K release ships as 24 per-chromosome VCF files (chr1-22, chrX,
+chrY). For the Genome Browser, these were concatenated with
<tt>bcftools concat</tt> into a single bgzip-compressed, tabix-indexed file.
</p>
<h2>Data Access</h2>
<p>
The VCF file for this track is available from
<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/ga4k/" target="_blank">our
download server</a> as <tt>ga4kSnv.vcf.gz</tt> (with <tt>.tbi</tt> index).
Regions can be extracted with <tt>tabix</tt>, for example:
<tt>tabix http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/ga4k/ga4kSnv.vcf.gz chr21:1-100000000</tt>.
</p>
<p>
The original per-chromosome VCFs and full release documentation are
available from the Children's Mercy Research Institute GA4K data release at
<a href="https://github.com/ChildrensMercyResearchInstitute/GA4K" target="_blank">
github.com/ChildrensMercyResearchInstitute/GA4K</a>.
</p>
<h2>Credits</h2>
<p>
Thanks to the Children's Mercy Research Institute and the Genomic Answers
-for Kids participants and their families for making this dataset publicly
-available.
+for Kids participants and their families, who released this dataset to the
+public.
</p>
<h2>References</h2>
<p>
Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L,
Baybayan P, Belden B <em>et al</em>.
<a href="https://linkinghub.elsevier.com/retrieve/pii/S1098-3600(22)00653-0" target="_blank">
Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes</a>.
<em>Genet Med</em>. 2022 Jun;24(6):1336-1348.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35305867" target="_blank">35305867</a>
</p>