f57e872b724de4bb82b14f07db837aeed4f5174a gperez2 Wed Jun 17 03:55:08 2026 -0700 Fix commas and update wording in varFreqs description pages. refs #37733 diff --git src/hg/makeDb/trackDb/human/varFreqsArray.html src/hg/makeDb/trackDb/human/varFreqsArray.html index b92b7fb5a94..0a8fed95a94 100644 --- src/hg/makeDb/trackDb/human/varFreqsArray.html +++ src/hg/makeDb/trackDb/human/varFreqsArray.html @@ -1,21 +1,21 @@ <h2>Description</h2> <p> This track merges variants from three genotyping-array cohorts into a single bigBed file with predicted protein consequences and cross-database filtering. It contains 14.7 million variants from the Taiwan Precision Medicine Initiative (TPMI Axiom TPM1 chip, -~1 million Han Chinese), the Mexico Biobank (MexBB, 6,011 individuals), and UK Biobank +~1 million Han Chinese), the Mexico Biobank (MexBB, 6,011 individuals), and the UK Biobank (361k unrelated white British, imputed from the Neale Lab Round 2 release). </p> <p> The array track is kept separate from the sequencing-based combined tracks (<a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> and <a href="hgTrackUi?g=varFreqsBackground">Population reference</a>) so that sequencing-based and array-based frequencies can be inspected independently. For a summary of all available variant frequency databases, see the <a href="hgTrackUi?g=varFreqs">SNV Frequencies</a> supertrack page. </p> <h2>Display Conventions</h2> <h3>Color by Consequence</h3> @@ -38,37 +38,37 @@ <h3>Amino Acid Change Notation</h3> <p> The "AA change" field uses bcftools csq notation: <b>23I>23V</b> means position 23 changed from Isoleucine (I) to Valine (V) (missense). <b>23I</b> alone (no arrow) means position 23 is Isoleucine and unchanged (synonymous). A "*" indicates a stop codon (e.g. 45R>45* is a stop_gained). </p> <h2>Caveats</h2> <p> Allele frequencies from genotyping arrays are not directly comparable to those from whole-genome or whole-exome sequencing. Two limitations to keep in mind: </p> <ul> - <li><b>Probe coverage is sparse and curated.</b> Array variants are only those the - manufacturer designed probes for. Absence from this track does <em>not</em> mean a + <li><b>Probe coverage is sparse and curated.</b> Array variants are only those for which the + manufacturer designed probes. Absence from this track does <em>not</em> mean a variant is absent in that population, only that it was not on the chip.</li> <li><b>Per-variant call confidence varies and is sometimes unreported.</b> TPMI publishes a per-probe <code>NGS_concordance</code> value (chip-vs-sequencing concordance from its own validation) in the source VCF; high-AF claims with low concordance are - common. MexBB ships only AN/AF/AC with no FILTER column and no per-site QC at all. + common. MexBB provides only AN/AF/AC with no FILTER column and no per-site QC. For both arrays, high-AF rare-disease candidates should be cross-checked against the sequencing-based <a href="hgTrackUi?g=varFreqsBackground">Population reference</a> track before drawing conclusions.</li> </ul> <h2>Filters</h2> <p> This track supports filtering via the track settings page. Click the track title or use the "Configure" button to access filters. </p> <h3>Variant Type and Consequence</h3> <ul> <li><b>Variant Type</b>: SNV, Insertion, Deletion, or MNV.</li>