Pangenome (HPRC) part 1: the graph's alleles and the haplotypes that have them

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.13. Desktop beta builds are coming soon.

The Human Pangenome Reference Consortium's release 2 builds 464 human haplotypes into a pangenome graph; the phased VCF used here lists 462 of them. Where the haplotypes differ, the graph forms a bubble, and each route through a bubble is an allele. HPRC writes each haplotype's route through every bubble as a phased VCF, so a record lists which haplotypes have which allele. We open the graph and the VCF from the HPRC page on genomes.jbrowse.org as tracks of a linear view of GRCh38, and:

read a whole chromosome, one node per bubble
at C4 (complement genes), read the graph's backbone, bubbles and alleles
at MHC class II, trace an allele beside HLA-DRB5 to the assembly it came from
list every haplotype with that allele from the VCF
back at C4, read the same alleles as aligned bases in HPRC's multiple alignment

Experimental

The graph view is a beta plugin, and the HPRC page launches it on the JBrowse 5 development build until JBrowse 5 ships. We welcome your feedback.

The graph and the page also leave real variation out, at some of the best-known loci in the genome. Read what they do not show before trusting an empty or simple picture.

Prerequisites

the GraphGenomeView plugin. In your own JBrowse, install it from the plugin store; every launch from the HPRC page already loads it
for the alignment on your own data: taffy

Where the data comes from

Nothing to download: the HPRC page's launches read the files of HPRC release 2, and our tabix index of its graph, by URL.

The files

the structural-variant graph (sv.gfa) the index files are cut from: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.sv.gfa.gz
the phased VCF, one record per allele, 462 haplotypes: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.pgbi.vcf.gz
the multiple alignment of every haplotype against GRCh38: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.full.maf.gz

Launching tracks from the HPRC page

Open the HPRC page. Click an Examples entry, or type a gene symbol or a region such as chr6:32,510,001-32,600,000 into the Gene or region box and press Show. The page draws the window in JBrowse, with a row of buttons choosing what it draws:

Graph: the region drawn as a graph, with the structural variants each haplotype has under it
Variants: the structural variants each haplotype has, over the genes
Haplotypes: one lane per structural form, commonest first
BandageJS: the same haplotypes in BandageJS

Open in full JBrowse opens the view shown in a tab of its own. Under the view, a sentence counts the structural forms the 464 haplotypes fall into in the window, and a Lane / Structure / Haplotypes / Share table names the haplotype that stands for each form, how the form differs from GRCh38 and how many share it. Haplotypes and BandageJS open those lanes. A window over 150 kb offers the graph alone.

The HPRC page answering its HLA / MHC example: the Gene or region box and its examples, then the Graph view drawn in the page and the structural forms its haplotypes have. The boxed button is Graph. Open the HPRC page ↗ (large dataset — this session takes a while to load)

What the graph and the page do not show

The examples are loci where at least one launch draws something readable. At other loci, a picture that looks simple or empty is often one of the cases below. We measured each on HPRC release 2.1 in October 2026.

Near-identical duplications draw as a single thread. The graph puts the copies at RHD / RHCE and CYP2D6 on one path, so those examples offer no Graph launch. SMN1 / SMN2, SRGAP2 and the 8p23.1 beta-defensin cluster are not examples at all: the graph over each is a thread, and no launch showed their copy number. A gene-level graph is the better tool for that question.
The graph does not align every haplotype everywhere. A haplotype the graph does not align across a window gets no lane, and the page counts them: "116 haplotypes are not aligned at any of them and have no lane" at FLNA / EMD, where those are the haplotypes without an X chromosome. Elsewhere the sequence exists in the assembly and the graph leaves it out. At NPHP1, 326 of the 462 haplotypes are aligned at two of the window's four sites and not at the rest, so the commonest lane reads "not aligned at 2 sites".
The VCF has no record for the largest events. HPRC removes every site with an allele over 100 kb from the VCF and keeps the smaller sites nested inside it. The Variants launch therefore cannot show UGT2B17's 117 kb deletion, which 229 haplotypes have. AMY1, GYPA / GYPB, PRSS1 / PRSS2, UGT2B17 and NPHP1 offer no Variants launch, because the matrix over each is blank. The page's table restores those sites from the release's unfiltered VCF, so the table can name a deletion the Variants launch does not draw.
The Structure column is a summary. A size is rounded to two figures, and a state fewer than 5 haplotypes have is folded into the commonest one. At a complex locus a row reads "14 size changes, largest a 10 kb deletion", which says little, and the HLA / MHC example has 34 forms of which the commonest holds 11% of haplotypes and the page lists 8. Two rows can have the same words for changes at different sites: four of PRSS1 / PRSS2's lanes read "20 kb insertion".
A size in the table can be wrong where sites nest. A restored site's size is what the sites inside it leave unexplained. That subtraction checked out for 92.5% of the cases we could test and gave a size the haplotype does not have in 189, most of them at 8p23.1.
Only the examples are checked. We looked at every launch of every example. A gene or region you type can still land where the graph is a thread or the VCF is blank, and the page will offer the launch anyway.
No single launch shows the whole locus. The graph shows which sequence exists, the VCF which haplotypes have it, and the lanes how a few haplotypes are arranged. Reading a locus means opening more than one.

Overview of chr1 with one node per variant region

Press chr1 among the Whole chromosomes links under the box. Zoomed out past the graph adapter's coarse level, JBrowse draws one node per bubble, so the whole chromosome fits. A curve of segments per bubble (how many pieces of sequence each bubble holds) shows how much the haplotypes disagree at each locus.

GRCh38 chr1 with the cytogenetic bands, three loci the HPRC pages open, and two tracks built from the graph's bubbles. The blue curve is segments per bubble; the second track draws one node per bubble as gold blocks. The blank column is 1q12, where nothing aligns.

Hosting your own graph builds this overview and writes the coarse slot.

The C4 locus as a graph

Click the HLA / MHC example on the HPRC page, then Open in full JBrowse. The Graph view opens three tracks: genes, the graph in the force-directed layout, and under it a matrix of the structural variants each haplotype has, one row per haplotype. Then:

Hide the variant matrix in the track selector, leaving the genes over the graph.
Type C4A in the location box, pick the chr6 hit, and zoom out twice to take in C4B.

The C4 locus as a force-directed graph under the hg38 genes for the same window, colored by reference position. The labels name a backbone segment, an allele, and a bubble whose two routes are the reference path and the dashed arc that skips one whole copy of the tandem C4-CYP21-TNX module.

The graph has four kinds of object:

the backbone is GRCh38's path, colored red to magenta by reference position
a bubble is a place where haplotypes disagree
an allele is a haplotype's sequence in place of the reference, drawn in charcoal because it has no reference position
an edge that skips sequence is a deletion, drawn as a dashed arc

Opening the haplotype the HLA-DRB5 allele came from

Type chr6:32,500,000-32,560,000, a window in MHC class II, a cluster of immune-system HLA genes. Beside HLA-DRB5, a charcoal node is an allele much shorter than the backbone stretch it hangs across. Left-click it. Its details give contributingHaplotype, NA20809#2: the graph's SN tag records which assembly minigraph first took the allele from.

Open in appears when the session has an assembly named or aliased sample#haplotype, the graph's name for it. The launch's config declares every release 2 haplotype that way. To declare one, load its contig sizes (or FASTA) under a display name, with the graph's name as an alias:

Config file

Goes in the assemblies array of config.json. See Assemblies.

{
  "name": "NA20809.2",
  "aliases": ["NA20809#2"],
  "uri": "https://jbrowse.org/pangenome/hprc-grch38/NA20809.2.chrom.sizes"
}

CLI (add-assembly)

jbrowse add-assembly https://jbrowse.org/pangenome/hprc-grch38/NA20809.2.chrom.sizes \
  --name NA20809.2 \
  --alias "NA20809#2"

Right-click the allele and take Open in NA20809.2. A second linear view opens below the first, on that haplotype's chromosome 6, framed on the allele with its CAT (Comparative Annotation Toolkit) gene annotation. Zoom out a few steps.

First, MHC class II in the force-directed layout, the NA20809.2 allele ringed with its right-click menu open on Open in NA20809.2. Second, the view that entry opens, NA20809 haplotype 2's chromosome 6 with its CAT genes.

The haplotype's CAT annotation has HLA-DRB9 and HLA-DRB6 either side of the allele and no HLA-DRB5, the gene it hangs across on hg38.

Listing every haplotype with the HLA-DRB5 allele

The graph names one source assembly per allele. HPRC's phased VCF lists every haplotype's allele at every bubble: a record is one allele written against GRCh38, and each sample's genotype holds a 1 for each of its haplotypes with that allele. We'll add it to the graph launch's session:

Config file

Goes in the tracks array of config.json. See Tracks.

{
  "type": "VariantTrack",
  "trackId": "hprc2_pgbi_grch38",
  "name": "HPRC release 2 phased VCF, one record per allele (462 haplotypes)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.pgbi.vcf.gz",
    "fetchSizeLimit": 20000000
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "unit": "haplotype",
      "filter": ["jexl:alleleLength(feature)>=50"]
    }
  ]
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "hprc2_pgbi_grch38",
  "name": "HPRC release 2 phased VCF, one record per allele (462 haplotypes)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.pgbi.vcf.gz",
    "fetchSizeLimit": 20000000
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "unit": "haplotype",
      "filter": ["jexl:alleleLength(feature)>=50"]
    }
  ]
}'

In the app

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "VariantTrack",
  "trackId": "hprc2_pgbi_grch38",
  "name": "HPRC release 2 phased VCF, one record per allele (462 haplotypes)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.pgbi.vcf.gz",
    "fetchSizeLimit": 20000000
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "unit": "haplotype",
      "filter": ["jexl:alleleLength(feature)>=50"]
    }
  ]
}

Open in JBrowse

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

unit: "haplotype" draws one row per haplotype.
filter drops records, and alleleLength(feature)>=50 keeps alleles of 50 bp and up, the size of the bubbles minigraph draws. alleleLength is the length of the record's longest allele, so it counts an insertion's inserted bases.
fetchSizeLimit raises the download cap past its default. The VCF spells out each inserted allele, which puts the MHC class II window over the default.
Filter by... → Edit filters... in the track menu shows the filter and changes it.
Advanced → Edit plot... in the track menu shows unit and filter as text and applies edits live.

Take Clustering → Cluster rows by genotype... in the track menu and press Run clustering. The rows reorder so haplotypes with the same alleles sit together, with a dendrogram beside them.

The 462-haplotype VCF at MHC class II clustered from the track menu: Clustering, Cluster rows by genotype, Run clustering, and the rows arriving in their new order with a dendrogram beside them.

Video

Open the session the video starts in ↗, then take the steps it shows:

Cluster the haplotypes by genotype from the track menu
Haplotypes with the same alleles now gather into blocks

Steps

Open this view in JBrowse Web ↗ · Open this view in JBrowse Desktop ↗

Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fhprc.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr6%3A32%2C510%2C000-32%2C600%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hg38_ncbiRefSeq_ucsc%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22displayMode%22%3A%22compact%22%2C%22height%22%3A60%7D%2C%7B%22trackId%22%3A%22hprc_minigraph_segments%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showLabels%22%3A%22none%22%2C%22heightMode%22%3A%22grow%22%2C%22color%22%3A%22jexl%3Aget%28feature%2C%27rank%27%29%3E0+%3F+%27rgb%2860%2C65%2C72%29%27+%3A+%27hsl%28%27+%2B+min%28300%2C+max%280%2C+%28%28get%28feature%2C%27start%27%29%2Bget%28feature%2C%27end%27%29%29%2F2+-+32510000%29+%2F+90000+*+300%29%29+%2B+%27%2C70%25%2C50%25%29%27%22%7D%2C%7B%22trackId%22%3A%22hprc2_pgbi_grch38%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22showVariantLane%22%3Atrue%2C%22height%22%3A340%2C%22filter%22%3A%5B%22jexl%3AalleleLength%28feature%29%3E%3D50%22%5D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fhprc_cluster_callset

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38.
Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq genes (hg38)”.
1. Track menu → Gene glyph → Representative transcript
2. Track menu → Feature height → Compact
Add the next track the same way.This figure uses “HPRC v2.1 graph (rGFA segments)”.
1. Track menu → Show... → Labels → None
2. Track menu → Feature height → Track sizing → Fixed feature height + autogrow track height
3. Track menu → Settings → colorA per-feature expression. The Color by... radios write a solid color, a field's palette, and the strand colors only, so an expression is authored on the track config.
Add the next track the same way. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “HPRC release 2 phased VCF, one record per allele (462 haplotypes)”.
1. Track menu → Show... → Show variant lane (checked)Draws the variants at their genomic positions in a lane above the genotype rows. Offered only while "Show as genotype matrix" is unchecked.
2. Track menu → Filter by... → add the expressionThis figure filters on alleleLength(feature)>=50.
Type your region of interest into the location box and press Enter.This figure is at chr6:32,510,000-32,600,000.

Spec

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/hprc.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr6:32,510,000-32,600,000",
      "tracks": [
        {
          "trackId": "hg38_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "displayMode": "compact",
          "height": 60
        },
        {
          "trackId": "hprc_minigraph_segments",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "heightMode": "grow",
          "color": "jexl:get(feature,'rank')>0 ? 'rgb(60,65,72)' : 'hsl(' + min(300, max(0, ((get(feature,'start')+get(feature,'end'))/2 - 32510000) / 90000 * 300)) + ',70%,50%)'"
        },
        {
          "trackId": "hprc2_pgbi_grch38",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 340,
          "filter": [
            "jexl:alleleLength(feature)>=50"
          ]
        }
      ]
    }
  ]
}

Agent

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr6:32,510,000-32,600,000",
      "tracks": [
        {
          "trackId": "hg38_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "displayMode": "compact",
          "height": 60
        },
        {
          "trackId": "hprc_minigraph_segments",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "heightMode": "grow",
          "color": "jexl:get(feature,'rank')>0 ? 'rgb(60,65,72)' : 'hsl(' + min(300, max(0, ((get(feature,'start')+get(feature,'end'))/2 - 32510000) / 90000 * 300)) + ',70%,50%)'"
        },
        {
          "trackId": "hprc2_pgbi_grch38",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 340,
          "filter": [
            "jexl:alleleLength(feature)>=50"
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/hprc.json \
  --width 1920 --height 880 \
  --spec session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Right-click the charcoal allele beside HLA-DRB5 in the force-directed graph and take Highlight in hg38: a band marks the span of GRCh38 it replaces, which covers most of HLA-DRB5.

The VCF and the graph in one window. The band is the span the HLA-DRB5 allele replaces, over every haplotype clustered by genotype: blue where a haplotype has an allele of 50 bp or more. Below, the force-directed graph, where an arrow runs from the band to the same allele as the graph draws it, alleles in charcoal.

The VCF holds the HLA-DRB5 allele as four records, one for each of its sequences, which differ by a base or two. The blue block under the band is the haplotypes with any of the four, plus a smaller block with an 86 kb deletion that removes the whole stretch.

Reading C4's alleles as aligned bases

HPRC also publishes its alignment as hprc-v2.1-mc-grch38.full.maf.gz, a multiple alignment with one row of bases per haplotype. A .tai index beside the 53 GB file makes a locus one ranged read:

Config file

Goes in the tracks array of config.json. See Tracks.

{
  "type": "MafTrack",
  "trackId": "hprc_v2_1_mc_grch38",
  "name": "HPRC release 2 pangenome alignment (464 haplotypes)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BgzipMafAdapter",
    "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.full.maf.gz"
  }
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "MafTrack",
  "trackId": "hprc_v2_1_mc_grch38",
  "name": "HPRC release 2 pangenome alignment (464 haplotypes)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BgzipMafAdapter",
    "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.full.maf.gz"
  }
}'

In the app

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "MafTrack",
  "trackId": "hprc_v2_1_mc_grch38",
  "name": "HPRC release 2 pangenome alignment (464 haplotypes)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BgzipMafAdapter",
    "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.full.maf.gz"
  }
}

Open in JBrowse

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

The uri shorthand resolves the sibling .tai. For a MAF of your own, taffy writes the index beside it:

# writes alignment.maf.gz.tai, which the adapter finds by its name
taffy index -i alignment.maf.gz

Go back to the C4 window, chr6:31,980,000-32,050,000, with the genes, the VCF and this alignment over the graph track. A white stretch in an alignment row is sequence that haplotype lacks. Then:

Clustering → Cluster rows by genotype... on the VCF orders its rows.
Clustering → Cluster rows by identity... on the alignment clusters over the window in view, because HPRC's file ships no guide tree.
Reset row order restores the order in the file.

C4 with the RefSeq genes, the VCF's haplotypes clustered by genotype, a subtree of them as alignment rows clustered by identity, and the graph track in the force-directed layout. The band marks the pseudogene pair between C4A and C4B, and the haplotypes with no sequence across the module gather into one block.

The VCF's widest blue block is one record, a deletion of a whole C4-CYP21-TNX module, which is the dashed arc in the C4 graph. Every alignment row in the white block has that deletion in the VCF. The narrower blocks are the 6.4 kb HERV-K (endogenous retrovirus) insertion in a C4 gene's intron, the difference between a long and a short C4. The configured track draws all the alignment rows.

Reproduce it end to end

Hosting your own graph builds the index files and the bubbles track in one command that runs on any rGFA. Run on hprc-v2.1-mc-grch38.sv.gfa.gz, it writes the files we host, and README.txt beside them records their provenance. For a graph of your own, minigraph can list each assembly's route through every bubble; see Which haplotypes pass through each segment.

External links

Li H. The rGFA format and gfatools, which define the SN/SO/SR tags this page opens the graph by, and whose bubble subcommand calls the bubbles it reads.
taffy, which writes the .tai index that makes the alignment addressable by locus.

Citations

HPRC release 2, the release this page opens: the Minigraph-Cactus graph, the multiple alignment and the VCFs vg deconstruct writes from the graph.

Feedback on this tutorial is welcome: contact us.

Pangenome (HPRC) part 1: the graph's alleles and the haplotypes that have them

Prerequisites#

Where the data comes from#

Launching tracks from the HPRC page#

What the graph and the page do not show#

Overview of chr1 with one node per variant region#

The C4 locus as a graph#

Opening the haplotype the HLA-DRB5 allele came from#

Listing every haplotype with the HLA-DRB5 allele#

Reading C4's alleles as aligned bases#

Reproduce it end to end#

See also#

External links#

Citations#

Prerequisites

Where the data comes from

Launching tracks from the HPRC page

What the graph and the page do not show

Overview of chr1 with one node per variant region

The C4 locus as a graph

Opening the haplotype the HLA-DRB5 allele came from

Listing every haplotype with the HLA-DRB5 allele

Reading C4's alleles as aligned bases

Reproduce it end to end

See also

External links

Citations