68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa lrnassar Mon Jun 1 14:40:45 2026 -0700 varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642 diff --git src/hg/makeDb/trackDb/human/meiSwegen.html src/hg/makeDb/trackDb/human/meiSwegen.html index e628b81ed32..306855a3594 100644 --- src/hg/makeDb/trackDb/human/meiSwegen.html +++ src/hg/makeDb/trackDb/human/meiSwegen.html @@ -1,169 +1,169 @@ <h2>Description</h2> <p> This track shows <b>mobile element insertions (MEIs)</b> identified by <a href="https://melt.igs.umaryland.edu/" target="_blank">MELT</a> on the <a href="https://swefreq.nbis.se/dataset/SweGen" target="_blank">SweGen</a> cohort of 1,000 Swedish whole-genome samples (Ameur et al. 2017). Each site is an insertion of an Alu, L1 (LINE-1), SVA or HERV-K mobile element relative to the reference. The SweGen short-variant frequency data for the same cohort is shown in the <a href="hgTrackUi?g=swegen">SweGen variant frequencies</a> subtrack of -the Variant Frequencies collection. +the SNV Frequencies collection. </p> <table class="stdTbl"> <tr><th>Class</th><th>MEIs</th></tr> <tr><td>Alu</td><td>14,467</td></tr> <tr><td>L1</td><td>2,429</td></tr> <tr><td>SVA</td><td>1,131</td></tr> <tr><td>HERVK</td><td>73</td></tr> <tr><th>Total (GRCh37)</th><th>18,100</th></tr> <tr><th>Total (after liftOver to hg38)</th><th>18,090</th></tr> </table> <p> For each MEI, the track reports the mobile element class, the insertion length, the MELT subfamily call (e.g. AluYa5, L1Ta), the target-site duplication sequence, the MELT ASSESS quality score, nearby gene context if the insertion lies in or close to a gene, the allele count (MELT_AN; despite the name this is the number of allele observations, not the allele number), the alt-allele frequency, and the MELT FILTER status. </p> <h2>Display Conventions and Configuration</h2> <p> An insertion has zero length on the reference: it attaches between two adjacent reference bases without replacing any of them. Following the convention used by MELT and by the other MEI tracks in this collection, each MEI is drawn as a <b>1-bp block sitting on the anchor base</b> — the reference base immediately to the left of the insertion attachment point. The inserted mobile element itself is not present in the reference and is therefore not drawn. The item label is <tt>class-altAlleleCount</tt>. </p> <p> Items are colored by element class: </p> <ul> <li><span style="display:inline-block;background-color:#0072B2;width:18px;height:12px;vertical-align:middle;"></span> <b>Alu</b> — SINE (Short INterspersed Element)</li> <li><span style="display:inline-block;background-color:#D55E00;width:18px;height:12px;vertical-align:middle;"></span> <b>L1</b> — LINE-1 (Long INterspersed Element-1)</li> <li><span style="display:inline-block;background-color:#009E73;width:18px;height:12px;vertical-align:middle;"></span> <b>SVA</b> (SINE-VNTR-Alu) — composite retrotransposon</li> <li><span style="display:inline-block;background-color:#CC79A7;width:18px;height:12px;vertical-align:middle;"></span> <b>HERVK</b> (Human Endogenous Retrovirus K) — endogenous retrovirus</li> </ul> <p> The score column encodes the alt-allele frequency on a 0-1000 scale. Filters allow restricting items by element class, insertion length, allele frequency, MELT ASSESS quality score (0-5) and the MELT FILTER status. The track keeps both PASS and non-PASS sites; non-PASS sites carry one of the MELT site-level filter codes: </p> <ul> <li><tt>s25</tt> — more than 25% of samples have no data at the site</li> <li><tt>rSD</tt> — ratio of left-side to right-side discordant pairs is more than two standard deviations from the mean</li> <li><tt>hDP</tt> — more discordant pairs at the site are also split-read than expected</li> </ul> <h2>Methods</h2> <p> The SweGen project sequenced 1,000 Swedish individuals on Illumina HiSeq X with 150 bp paired-end reads (Covaris E220 fragmentation, ~350 bp insert), and aligned the reads to the GRCh37 reference with BWA-MEM v0.7.12. Mobile element insertions were called by <a href="https://melt.igs.umaryland.edu/" target="_blank">MELT</a> v2.0.2 (Gardner et al. 2017) in MELT-Split mode using the default ALU, HERVK, LINE1 and SVA mobile-element zip packages, on all 1,000 samples. Per-site allele counts and frequencies (MELT_AN and MELT_AF in INFO) were computed across the cohort; the VCF does not contain per-sample genotype columns. The analysis used the Perl SMELT pipeline (<a href="https://github.com/J35P312/SMELT" target="_blank">github.com/J35P312/SMELT</a>) on the UPPMAX Bianca cluster in early 2018, by Diana Ekman, Jesper Eisfeldt and Daniel Nilsson. </p> <p> The site-level VCF <tt>MELT_SWEGEN.20180314.ALU_HERVK_LINE1_SVA.vcf</tt> was obtained from the SweGen download portal (<a href="https://swefreq.nbis.se/dataset/SweGen/download" target="_blank">swefreq.nbis.se/dataset/SweGen/download</a>, access requires a brief approval). The VCF uses GRCh37 contigs without a "chr" prefix; the conversion adds the prefix, drops the VCF header, maps SVTYPE codes (<tt>ALU</tt>, <tt>LINE1</tt>, <tt>SVA</tt>, <tt>HERVK</tt>) to the element class names used here, copies INFO fields through to the BED, and writes a bed9+9 file with 1-bp anchor intervals. The hg19 BED was then lifted to hg38 with UCSC <tt>liftOver</tt> (<tt>-tab -bedPlus=9</tt>), which mapped 18,090 of 18,100 records; 10 records fell into hg38-deleted regions and were dropped. The lifted BED was sorted and converted to bigBed using the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/mei/meiSwegen.as" target="_blank">meiSwegen.as</a> schema. Conversion and lift steps are documented in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/mei.txt" target="_blank">makeDoc file</a>; the scripts live in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/mei" target="_blank">src/hg/makeDb/scripts/mei</a>. </p> <h3>Why the original GRCh37 MELT VCF rather than the GRCh38 SVDB files</h3> <p> The SweGen download portal also distributes a hg38 variant set (<tt>SweGen38_{ALU,L1,SVA,HERV}.vcf</tt>) for the same 1,001 samples, produced with SVDB after re-running on GRCh38. We chose to lift the original GRCh37 MELT VCF instead because the hg38 SVDB files contain 138,853 records (about 7.7× the MELT site count), and roughly 60% of those records are singletons (<tt>OCC=1</tt>) without any quality filter. They also drop most of the per-site annotation: no MELT subfamily call (e.g. AluYa5, L1Ta), no insertion length (<tt>SVLEN=0</tt> everywhere), no target-site duplication, no MELT ASSESS quality score, no gene context and no FILTER stratification (every site is marked <tt>PASS</tt>). The GRCh37 MELT VCF, lifted to hg38, gives a much more informative and quality-filtered set, at the cost of 10 records that fell into hg38-deleted regions. </p> <h2>Data Access</h2> <p> Due to SweGen license restrictions, the underlying VCF and the bigBed derived from it cannot be redistributed from the UCSC Genome Browser. The Table Browser and download server are disabled for this track. To obtain the source data, follow the request procedure at the <a href="https://swefreq.nbis.se/dataset/SweGen" target="_blank">SweGen download portal</a>. </p> <h2>Credits</h2> <p> Thanks to Adam Ameur, Diana Ekman, Jesper Eisfeldt, Daniel Nilsson and the SweGen consortium for generating and releasing the MELT MEI callset, and to SciLifeLab for producing the underlying SweGen WGS data. </p> <h2>References</h2> <p> Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kähäri AK, Lundin P, Che H <em>et al</em>. <a href="https://doi.org/10.1038/ejhg.2017.130" target="_blank"> SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population</a>. <em>Eur J Hum Genet</em>. 2017 Nov;25(11):1253-1260. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28832569" target="_blank">28832569</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765326/" target="_blank">PMC5765326</a> </p> <p> Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, 1000 Genomes Project Consortium, Devine SE. <a href="http://genome.cshlp.org/lookup/pmidlookup?view=long&pmid=28855259" target="_blank"> The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology</a>. <em>Genome Res</em>. 2017 Nov;27(11):1916-1929. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28855259" target="_blank">28855259</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668948/" target="_blank">PMC5668948</a> </p>