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/finngen.html src/hg/makeDb/trackDb/human/finngen.html new file mode 100644 index 00000000000..80e1daa8335 --- /dev/null +++ src/hg/makeDb/trackDb/human/finngen.html @@ -0,0 +1,56 @@ +<h2>Description</h2> +<p> +<a href="https://www.finngen.fi/en" target="_blank">FinnGen</a> is a public-private partnership +that combines genotype data from Finnish biobanks with digital health record data from Finnish +health registries. The R12 release contains imputed variants from 500,348 biobank samples obtained +using genotyping arrays. The imputation used phased variants obtained from 8,554 high-quality +whole genome sequences, also from Finland. This represents approximately 10% of the Finnish +population. Phenotype links can be viewed at the +<a href="https://r12.finngen.fi/" target="_blank">FinnGen PheWeb</a>. +</p> + +<h2>Data Access</h2> +<p> +Due to license restrictions, the data for this track cannot be downloaded from the UCSC +Genome Browser. The Table Browser, Data Integrator, and download server are not available +for this track. +</p> +<p> +TSV data can be requested via the form at +<a href="https://finngen.gitbook.io/documentation/data-download" target="_blank">FinnGen</a>, +which triggers an automated email containing the download link. +A script in our Github repo converts this file to VCF (see Methods below). +</p> + +<h2>Methods</h2> +<p> +FinnGen participants were genotyped using a custom Axiom FinnGen1 array, supplemented by legacy +collections genotyped with other arrays. Imputation used a population-specific reference panel of +high-coverage (25–30x) whole-genome sequences from Finnish individuals. Ancestry outliers were +removed via PCA against 1000 Genomes reference samples, and 5,780 duplicates and monozygotic twins +were excluded. Variant quality was assessed using VQSR. +</p> +<p> +R12 annotated variants were downloaded from the Google Cloud bucket link received through an email +and converted to VCF with a +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/finngen_to_vcf.py" +target="_blank">custom Python script</a>. +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> +We want to acknowledge the participants and investigators of the FinnGen study. +</p> + +<h2>References</h2> +<p> +Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, +Aavikko M, Kaunisto MA <em>et al</em>. +<a href="https://doi.org/10.1038/s41586-022-05473-8" target="_blank"> +FinnGen provides genetic insights from a well-phenotyped isolated population</a>. +<em>Nature</em>. 2023 Jan;613(7944):508-518. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36653562" target="_blank">36653562</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9849126/" target="_blank">PMC9849126</a> +</p>