This document summarizes the changes to the UCSC Genome Browser Hub TrackDb specification.
| Date | Track Types | Link to Doc | Change |
|---|---|---|---|
| 2026-07-31 | +faceted composite | +maxCheckboxes | +Documentation fix: this setting was previously listed here as
+ maxCheckBoxes, with a capital B. Setting names are case sensitive and the
+ browser has always read it as maxCheckboxes, so hubs that used the
+ capitalized spelling fell back to the default of 20 facet values. If your hub sets
+ maxCheckBoxes, change it to maxCheckboxes. |
+
| 2026-07-08 | genomes.txt setting | codonTable | New codonTable genome-stanza setting (an assembly hub
genomes.txt setting, not a track setting) assigns NCBI genetic
codes to individual sequences for amino acid display, e.g.
codonTable default=1 NC_017929.1=13. Affects the base position
track three-frame translation, codon-colored tracks such as gene
predictions, and details pages. Sequences named chrM/chrMT still default to
the vertebrate mitochondrial code. |
| 2026-06-02 | bigBed, bigGenePred | colorFields | New colorFields setting adds a Color by: dropdown to the
track controls page, letting users switch among multiple pre-computed color schemes
stored as extra bigBed fields containing R,G,B strings.
The special name default="label" renames the standard itemRgb option.
When a non-default scheme is selected, a (Coloring by: label) suffix
appears in the track long label. |
| 2026-05-08 | bed, bigBed | filterPriority / highlightPriority | New filterPriority.<fieldName> setting controls the
display order of filter controls on the track configuration page. A
companion highlightPriority.<fieldName> setting orders
highlight controls. |
| 2026-04-22 | faceted composite tracks | subtrackUrls | An update for the subtrackUrls option for faceted composites, which enables links out to other resources in the faceted table. |
| 2026-04-10 | vcf, vcfTabix, vcfPhasedTrio | sampleMetadataFile | Add per-sample metadata columns to the VCF genotype details table.
Points to a tab-separated file with a #sample header line;
columns are appended to the genotype table on the item details page. |
| 2026-04-08 | bigBed | detailsScript | Add custom JavaScript visualizations (e.g. histograms) to the item details page. An ES6 module is loaded on demand and renders into the extra fields table. First plot type: histogram, for logfmt-encoded allele frequency data. |
| 2026-03-09 | bigBed | faceted composite | An alternate UI for composite tracks with a very large number of subtracks. |
| 2026-01-12 | bigBed | style | Activates the positional heatmap display mode for a track that meets the schema. |
| 2026-01-11 | hic | hicArcLimit | Limit the number of arcs displayed in a Hi-C plot, favoring those with the highest scores |
| 2025-03-31 | interact, bigInteract | detailBoxesEnabled | Used to suppress the link/boxes in interact tracks that would go to a details page. |
| 2025-03-06 | hic | bigDataUrl | Added hic to the list of supported file types for bigDataUrl. |
| 2024-06-11 | bigBed, bigGenePred, bigChain, bigPsl | highlightValues.* | Allow user to highlight certain features in yellow, if they contain certain values in an extraField |
| 2024-01-22 | bigWig | setColorWith | Color a signal plot from a bigWig file by the ranges in a bigBed file |
| 2023-11-08 | bigBed, bigGenePred, bigChain, bigPsl | decorator.* | Semi-transparently overlay annotations, e.g. protein domains on transcripts, mutations on exons, or summits on chip-seq peaks |
| 2023-10-16 | bigGenePred, bigChain, bigPsl | mouseOver, mouseOverField | mouseOver works for all bigBed-based file formats |
| 2023-06-27 | all | maxItems | Change: maxItems, increased default to 10,000, 10x more items can be shown. |
| 2023-04-04 | all | downloadUrl | New: downloadUrl <fileType> <URL> Shows a link where user can download a file. On the UCSC browser, the link is shown above the description page. Right now this is used for GFF files on gene tracks. |
| 2022-09-30 | bigBed, BAM | doWiggle | New: doWiggle on Instead of showing the features, show coverage of features, as a 'wiggle' (signal) style track. Can be switched off by the user on the track config page. |
| 2022-09-22 | bigGenePred | colorByStrand | Change: colorByStrand can now be used by bigGenePred-type tracks. |
| 2022-06-30 | bigPsl, bigChain | otherTwoBitUrl | New: otherTwoBitUrl <URL> This statement allows one to store query sequences in a separate twoBit file rather than in the annotation file itself, which can reduce the size of the annotation file. |
| 2022-05-14 | bigWig | logo | New: logo on Motif logo of the genome sequence, as a "dynseq" display, see the example. |
| 2022-05-11 | genomes.txt setting | chromAuthority | New chromAuthority genome-stanza setting (an assembly hub
genomes.txt setting, not a track setting) chooses which
chromAlias name column is displayed by default for the
assembly's sequences, e.g. chromAuthority ucsc. |
| 2022-05-05 | bigMaf, maf | logoMaf | New: logoMaf on Motif logo on MAF/bigMaf alignment tracks. Zooming in on alignment shows nucleotides scaled by phyloP conservation. |
| 2019-05 | all | useOneFile | useOneFile on Adding the 'useOneFile on' line to the hub.txt section of a hub allows the contents of all three files to be referenced inside of one file. |