fa8084416354441c8c817069b7f92344f833d8dc max Tue Sep 8 01:13:43 2026 -0700 hprc2annot: say in the pcLAI docs that uniform color is the expected case Two of us in a row zoomed a pcLAI track to a few megabases, saw a single flat color, and concluded the itemRgb was broken. It is not: pclai.bb for GCA_046629565.1 holds 258 distinct RGB values, but 25,416 of its 25,438 windows sit in one tight cluster in PCA space (PC1 ~0.40-0.44) and so map to one tight cluster in color space, R 203-255 G 149-164 B 255, which is a couple of perceptual steps wide. The color column is a byte-for-byte pass-through of the HPRC source BED, verified against the S3 file. Two things the page did not say. A haplotype with one ancestry throughout is uniform across every chromosome and that is the correct render. And where a haplotype does carry several ancestries, the blocks are tens of megabases long, so any view narrower than a chromosome tends to land inside one block and look uniform too. Add an example so this is checkable rather than asserted: GCA_018466835.2 (HG02257) has four segment-level ancestry calls, and its chr17 crosses four blocks with transitions near 10.0, 50.7 and 73.3 Mb. Name the three chromosomes in that same assembly, chr2 chr13 chr18, that are single-ancestry end to end, since chr2 is the one that started this. refs #35415 diff --git src/hg/makeDb/trackDb/contrib/hprc2annot/pclai.html src/hg/makeDb/trackDb/contrib/hprc2annot/pclai.html index 3d597d26f6a..0b71117dab3 100644 --- src/hg/makeDb/trackDb/contrib/hprc2annot/pclai.html +++ src/hg/makeDb/trackDb/contrib/hprc2annot/pclai.html @@ -1,85 +1,106 @@ <h2>Description</h2> <p> This track shows pangenome local ancestry inference (pcLAI) for this Human Pangenome Reference Consortium (HPRC) Release 2 assembly, in the assembly's own coordinates. Every person's genome is a mosaic inherited from ancestors of different populations, and "local ancestry" describes, region by region along a chromosome, where a stretch of DNA came from. Rather than picking one population label per region, pcLAI places each region on a continuous scale, so ancestry that sits between two reference populations is not forced into one of them. This track divides each haplotype into windows of about a hundred thousand bases and reports the ancestry inferred for each one, letting users see how ancestry varies along a single individual's genome. </p> <h2>Display Conventions</h2> <p> Each item is one genomic window. Items carry no visible label. Holding the mouse over an item shows the window identifier, the position of the window in the principal-component space that pcLAI uses to describe ancestry, the position of the longer ancestry segment the window belongs to, and a confidence score; the same values are on the details page. The item color is derived from the same principal-component position, so windows of similar inferred ancestry get similar colors and a run of shared ancestry appears as a block of consistent color. Because the color is continuous rather than a set of population labels, it is read by comparing regions with each other rather than against a fixed legend. </p> <p> +The color follows the ancestry segment rather than the individual window, so +neighboring windows inside one segment differ by only one or two color steps. +Those small differences are not meaningful: the feature to read is the block, not +the window. Two consequences are worth knowing before concluding that a display +looks wrong. First, a haplotype with a single ancestry throughout gives one +uniform color across every chromosome, which is the correct result for that +sample rather than a rendering problem. Second, where a haplotype does carry +several ancestries the blocks are tens of megabases long, so a view of only a few +megabases usually falls inside one block and also looks uniform. Zooming out to a +whole chromosome is what makes the block structure visible. +</p> +<p> +Assembly <tt>GCA_018466835.2</tt> (sample HG02257) is a useful example of a +haplotype with several ancestry segments. Its <tt>chr17</tt> crosses four blocks, +with transitions near 10.0 Mb, 50.7 Mb and 73.3 Mb, and <tt>chr5</tt> crosses +four more across its 184 Mb; <tt>chr20</tt> and <tt>chr22</tt> each cross three. +In that same assembly <tt>chr2</tt>, <tt>chr13</tt> and <tt>chr18</tt> carry a +single ancestry from end to end and are uniform in color, so picking one of those +chromosomes gives no sense of what the track shows. +</p> +<p> The track is best viewed in pack mode. In dense mode the windows are collapsed onto one row, which hides the per-window values. </p> <h2>Methods</h2> <p> Conventional local ancestry inference gives every segment of a genome one of a fixed set of population labels. Point cloud local ancestry inference instead places each segment at a point in a continuous coordinate space, so a genome becomes a cloud of points, one per haplotype segment. The coordinate space can be any continuous description of ancestry; here it is the first two principal components of a reference panel of genomes with known population of origin. Ancestry that falls between the reference populations, which a label-based method has to round to the nearest label, therefore stays visible as an intermediate position. The files carry both the coordinate of each individual window and the coordinate of the longer ancestry segment that window belongs to. See the reference below for the method. This track uses the assembly-coordinate (<tt>asm_coord</tt>) output, that is, ancestry placed on each HPRC assembly's own sequence; companion outputs projected onto GRCh38 and CHM13 coordinates are distributed separately. </p> <p> The annotation files were obtained from the HPRC Release 2 data collection on the public <tt>s3://human-pangenomics</tt> bucket, indexed at <a href="https://github.com/human-pangenomics/hprc_intermediate_assembly/tree/main/data_tables/annotation/pclai" target="_blank">the hprc_intermediate_assembly data tables</a>. The per-assembly BED file was converted to a UCSC bigBed file, with the window identifier and the two sets of coordinates split out of the source item name into their own fields. The steps are described in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/contrib/hprc2annot.txt" target="_blank">makeDoc</a>, the build scripts are in the <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/hprc2annot" target="_blank">kent source tree</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/trackDb/contrib/hprc2annot" target="_blank">trackDb/contrib/hprc2annot</a>. Every window in the source files is carried through to the bigBed. </p> <h2>Data Access</h2> <p> For automated analysis, the annotation is stored in a bigBed-format file (<tt>pclai.bb</tt>) that can be read with the UCSC tool <tt>bigBedToBed</tt>. The original files are available from the HPRC S3 bucket linked above. </p> <h2>Credits</h2> <p> Annotations were generated by the Human Pangenome Reference Consortium. Thanks to the HPRC production team for making these data available. </p> <h2>References</h2> <p> Geleta M, Mas Montserrat D, Ioannidis NM, Ioannidis AG. <a href="https://doi.org/10.64898/2026.03.23.713813" target="_blank"> Point cloud local ancestry inference (PCLAI): continuous coordinate-based ancestry along the genome</a>. <em>bioRxiv</em>. 2026 Mar 25. doi: <a href="https://doi.org/10.64898/2026.03.23.713813" target="_blank">10.64898/2026.03.23.713813</a> </p>