aa61ebc800429515f9ced7e28f669c6042219f43 max Wed Mar 18 09:09:13 2026 -0700 varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/hgdp1kFreq.html src/hg/makeDb/trackDb/human/hgdp1kFreq.html new file mode 100644 index 00000000000..7897a903467 --- /dev/null +++ src/hg/makeDb/trackDb/human/hgdp1kFreq.html @@ -0,0 +1,79 @@ +<h2>Description</h2> +<p> +A reprocessed callset by the <a href="https://gnomad.broadinstitute.org/news/2021-10-gnomad-v3-1-2-minor-release/" +target="_blank">gnomAD project</a> combining the 1000 Genomes and Human Genome Diversity Project +(HGDP) data, with 4,094 whole genomes from 80 populations. The dataset includes per-population +allele frequencies for all 80 populations as well as broad continental groupings from gnomAD +(African, Admixed American, East Asian, European, Middle Eastern, South Asian, and others). +</p> + +<p> +This track shows allele frequencies only. The full phased genotype data with haplotype +clustering display is available in the +<a href="hgTrackUi?g=hgdp1k">gnomAD HGDP+1000G track</a> under Phased Variants. +The track here does not include the full variant frequencies for all subpopulations, instead, +it aggregates frequencies to the main groups, AFR, AMI, AMR, ASJ, EAS, FIN, MID, NFE, OTH, SAS. +To access the full frequency information, use the track under "Phased Variants". +</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 +track name is <em>hgdp1kFreq</em>. +For bulk download, the VCF file can be obtained from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/varFreqs/" target="_blank">our download server</a>. +</p> +<p> +The original VCFs with full genotypes can also be downloaded from +<a href="https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg" +target="_blank">gnomAD Downloads</a>. +</p> + +<h2>Methods</h2> +<p> +The gnomAD project reprocessed 4,094 whole genomes from the 1000 Genomes Project and the Human +Genome Diversity Project (HGDP) through a unified pipeline. Sequencing was performed on Illumina +platforms at a mean coverage of 32–34x. Reads were aligned to GRCh38 (hs38DH reference with +decoy and HLA sequences) using BWA-MEM 0.7.15. Variant calling followed GATK best practices: +per-sample calling with GATK 3.5 HaplotypeCaller followed by joint genotyping with GATK4 using +the Hail VCF combiner for scalable merging. Allele-specific variant quality score recalibration +(AS-VQSR) was applied for both SNPs and indels. Sample QC included contamination estimation +(verifyBamID), sex concordance, relatedness filtering (PC-Relate), and population assignment +using PCA against gnomAD reference panels. Per-population allele frequencies were computed for +80 fine-grained populations as well as broad continental groupings. +</p> +<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>Credits</h2> +<p> +Thanks to the gnomAD team at the Broad Institute for harmonizing and making this dataset +publicly available, and to all participants of the 1000 Genomes Project and the Human Genome +Diversity Project. +</p> + +<h2>References</h2> +<p> +Koenig Z, Yohannes MT, Nkambule LL, Zhao X, Goodrich JK, Kim HA, Wilson MW, Tiao G, Hao SP, Sahakian +N <em>et al</em>. +<a href="https://pmc.ncbi.nlm.nih.gov/articles/pmid/38749656/" target="_blank"> +A harmonized public resource of deeply sequenced diverse human genomes</a>. +<em>Genome Res</em>. 2024 Jun 25;34(5):796-809. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38749656" target="_blank">38749656</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216312/" target="_blank">PMC11216312</a> +</p> + +<p> +Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, Chen Y, Felkel S, Hallast P, Kamm J +<em>et al</em>. +<a href="https://www.science.org/doi/10.1126/science.aay5012" target="_blank"> +Insights into human genetic variation and population history from 929 diverse genomes</a>. +<em>Science</em>. 2020 Mar 20;367(6484). +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32193295" target="_blank">32193295</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115999/" target="_blank">PMC7115999</a> +</p>