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  Wed May 20 14:57:51 2026 -0700
varFreqs: add Genome of the Netherlands (GoNL) subtrack on hg38, GRCh38 re-analysis v1.0, 498 unrelated parents (250 fathers + 248 mothers), 36.4M biallelic records after dropping decoy/EBV contigs and bcftools norm split+left-align, refs #36642

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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+<h2>Description</h2>
+<p>
+The <a href="http://www.nlgenome.nl/" target="_blank">Genome of the Netherlands</a> (GoNL) is a
+whole-genome sequencing project covering the Dutch population. The cohort was drawn from five
+Dutch biobanks and includes 250 parent-offspring families (231 trios and 19 quartets) from 11 of
+the 12 Dutch provinces. Samples were not selected by phenotype or disease status. This track
+shows allele counts and frequencies from the GRCh38 re-analysis of GoNL, restricted to the 498
+unrelated parents (250 fathers and 248 mothers; two mothers failed QC in the original release).
+</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" target="_blank">REST API</a>
+can be used; the track name is <em>gonl</em>.
+For bulk download, the VCF is available from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/gonl/" target="_blank">our download
+server</a>. The original file is also available from
+<a href="https://download.molgeniscloud.org/downloads/gonl_public/variants/GoNL_GRCh38_1.0/"
+target="_blank">the GoNL download directory at MolGenis</a>.
+</p>
+
+<h2>Methods</h2>
+<p>
+The track shown here uses the GRCh38 re-analysis (version 1.0). All samples were re-aligned from
+raw reads to a GRCh38 analysis set (GRCh38_no_alt_plus_hs38d1 with PhiX as decoy). The processing
+pipeline is documented in the
+<a href="https://download.molgeniscloud.org/downloads/gonl_public/variants/GoNL_GRCh38_1.0/README.txt"
+target="_blank">README accompanying the data</a> and differs from the original Nature Genetics
+pipeline (reference below). Per-library reads were trimmed with cutadapt 1.13, aligned with bwa mem 0.7.15, sorted
+with Picard SortSam 2.9.0, and base-quality-recalibrated with GATK BaseRecalibrator 3.7. Per-sample
+files were merged and deduplicated with sambamba 0.6.6, and variants were called per sample with
+GATK HaplotypeCaller 3.7. Per-family GVCFs were merged with GATK CombineGVCFs, and all families
+were jointly genotyped with GATK GenotypeGVCFs 3.7. The GRCh38 callset has not been filtered with
+VQSR and missing genotypes have not been imputed, so it is rougher than the original GRCh37
+release.
+</p>
+<p>
+The file
+<tt>multisample.parents_only.info_only.vcf.gz</tt> was downloaded from
+<a href="https://download.molgeniscloud.org/downloads/gonl_public/variants/GoNL_GRCh38_1.0/"
+target="_blank">https://download.molgeniscloud.org/downloads/gonl_public/variants/GoNL_GRCh38_1.0/</a>.
+Of the 31,114,481 records in the source file, 30,904,161 were kept after dropping calls on the
+GRCh38 decoy contigs (chrUn_JTFH01* and similar) and the EBV contig, which are not part of the
+UCSC hg38 assembly. The original chromosome naming already uses the UCSC <tt>chr</tt> prefix, so
+no renaming was needed. The 2,629,361 multiallelic sites were then split with
+<tt>bcftools norm -m-any</tt>, with indels left-aligned against the hg38 reference, yielding
+36,363,474 biallelic records (3,559,402 indels realigned). The maximum observed allele number
+(AN) is 996, which matches the 498 diploid parents in the cohort. Loading documentation is in the
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt"
+target="_blank">varFreqs makeDoc file</a>; helper scripts for the broader varFreqs collection
+are in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs"
+target="_blank">our GitHub scripts directory</a>.
+</p>
+
+<h2>Credits</h2>
+<p>
+Data was generated by the Genome of the Netherlands Consortium and distributed via the
+<a href="https://www.molgenis.org/" target="_blank">MOLGENIS</a> infrastructure at the
+University Medical Center Groningen. Thanks to the participants who donated samples and to the
+BBMRI-NL biobanks: LifeLines, Leiden Longevity Study, Netherlands Twin Registry, Rotterdam Study
+and Rucphen Study.
+</p>
+
+<h2>References</h2>
+<p>
+Genome of the Netherlands Consortium.
+<a href="https://doi.org/10.1038/ng.3021" target="_blank">
+Whole-genome sequence variation, population structure and demographic history of the Dutch
+population</a>.
+<em>Nat Genet</em>. 2014 Aug;46(8):818-25.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24974849" target="_blank">24974849</a>
+</p>
+