Synteny between neighbouring haplotypes (the amylase locus)

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.8. Desktop beta builds are coming soon.

People carry different numbers of copies of AMY1, the salivary amylase gene, and the copies sit in a tandem array on chr1 that GRCh38 assembles with three. We find an assembled haplotype of each common structure, from one copy to seven, and align each to the one under it. A stack aligned to GRCh38 alone has nowhere to put a copy GRCh38 lacks. Aligned to its neighbour, a haplotype with two more copies differs from the one above it by a single insertion, which the linear synteny view draws from the alignment's CIGAR.

Prerequisites

samtools, built with libcurl, to fetch a region of a remote FASTA
minimap2
Node.js, for npx
python3
A running JBrowse instance (the web quickstart or the desktop quickstart)

Where the data comes from

HPRC release 2, whose assemblies are published as bgzipped, faidx-indexed FASTA, so one locus comes out of a 3 Gb assembly by range request, and whose graph is published as a database that answers a window over HTTP.

the release's Minigraph-Cactus graph as a gbz-base database, read by range request: 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.gbz.db
the companion index that names the database's haplotypes, which part 3 of the HPRC tutorial builds: https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.anchored.db
the assembly index, one row per haplotype with its FASTA: https://raw.githubusercontent.com/human-pangenomics/hprc_intermediate_assembly/main/data_tables/assemblies_release2_v1.0.index.csv
HG01361 haplotype 1: https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC/HG01361/assemblies/release2/HG01361_pat_hprc_r2_v1.0.1.fa.gz
HG00133 haplotype 1: https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC/HG00133/assemblies/release2/HG00133_hap1_hprc_r2_v1.0.1.fa.gz
NA18608 haplotype 2: https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC/NA18608/assemblies/release2/NA18608_hap2_hprc_r2_v1.0.1.fa.gz
HG00232 haplotype 1: https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC/HG00232/assemblies/release2/HG00232_hap1_hprc_r2_v1.0.1.fa.gz
GRCh38, bgzipped and indexed: https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz
every release 2 haplotype as an assembly of its chromosome lengths with its CAT gene annotation, one model per gene: https://jbrowse.org/pangenome/hprc-grch38/config.json
eight of those haplotypes aligned to GRCh38, which the pangenome graph synteny tutorial builds: https://jbrowse.org/demos/hprc_multiway/config.json
hg38's RefSeq genes, rehosted: https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz

The locus under GRCh38 alone

The pangenome graph synteny tutorial stacks eight HPRC haplotypes under hg38, each lane on its own contig with its own gene models. Open that stack over the amylase array:

Config file

{
  "defaultSession": {
    "name": "The amylase locus across eight HPRC haplotypes",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "hg38",
        "loc": "chr1:103,520,894-103,832,637",
        "tracks": [
          "hg38_ncbiRefSeq_ucsc",
          {
            "trackId": "hprc_multiway",
            "type": "MultiWaySyntenyDisplay",
            "height": 600
          }
        ]
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "The amylase locus across eight HPRC haplotypes",
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:103,520,894-103,832,637",
      "tracks": [
        "hg38_ncbiRefSeq_ucsc",
        {
          "trackId": "hprc_multiway",
          "type": "MultiWaySyntenyDisplay",
          "height": 600
        }
      ]
    }
  ]
}
EOF

URL

Open this session in JBrowse

The reference row holds AMY2B, AMY2A and three AMY1 copies, AMY1A, AMY1B and AMY1C. The lanes' own annotations disagree with it in both directions: HG00097.1 and HG00099.1 carry two AMY1 copies and HG00128.1 five, its lane drawn at half the scale of the others to fit them. Every alignment in this track joins a haplotype to GRCh38, so the copies HG00128.1 holds beyond the reference's three align to nothing, and the ribbon between two haplotype lanes is composed through the reference row.

The amylase locus on hg38 over eight HPRC haplotype lanes, each drawing its own CAT gene models. The two lanes at the bottom hold fewer amylase genes than the reference row, and the HG00128.1 lane at the top holds more and draws at a smaller scale. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

A haplotype of each structure

Yilmaz et al. 2024 name a structure at this locus by its gene counts: H and the AMY1 copies, then A and B with the AMY2A and AMY2B copies where either is not one. GRCh38 is their H3r.1, the reference arrangement, and the common structures run from H1a, a single copy, up through H5 and H7 in steps of two. None of the eight lanes above is an H1a or an H7.

The release's graph finds them among all of its haplotypes. A haplotype's walk crosses any single-copy window once, so its coordinate at a window left of the array and at one right of it gives its span across the array. gbz-base-query reads a window of the published database over HTTP and prints one record per haplotype, in that haplotype's own coordinates:

DB=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.gbz.db
INDEX=https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.anchored.db
# --haplotype-index names each walk's sample, haplotype and contig
# --context 0 reads the window alone, with nothing either side of it
# --alignments prints one record per haplotype, with its own coordinates
npx --yes -p @gmod/gbz-base gbz-base-query $DB --haplotype-index $INDEX \
  --sample GRCh38 --contig chr1 --interval 103540000..103541000 \
  --context 0 --alignments > left.json

The script runs it again at 103800000..103801000 and subtracts. The spans fall into classes one repeat unit apart, and counting the genes of a few haplotypes from each (below) names them:

Span against GRCh38's	Haplotypes	AMY1 copies	Structure
94 kb shorter	53	1	H1a
72 kb shorter	11	2, no AMY2A	H2A0
the same	232	3	H3r
94 kb longer	79	5	H5
188 kb longer	22	7	H7
282 kb longer	5	9	H9

The other 59 haplotypes with both windows on one contig sit between these classes or past them.

Aligning each haplotype to its neighbour

Five rows make the stack, in order of AMY1 copies: HG01361.1 with one, GRCh38 and HG00133.1 with three, NA18608.2 with five and HG00232.1 with seven. The two coordinates from the step above frame each haplotype's copy of the locus, and samtools faidx reads a region of a remote bgzipped FASTA through its .fai and .gzi, so each row is one request:

HPRC=https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC
samtools faidx \
  $HPRC/HG00232/assemblies/release2/HG00232_hap1_hprc_r2_v1.0.1.fa.gz \
  'HG00232#1#CM089991.1:103491008-103991760' > HG00232.1.fa

Each row is then aligned to the row under it:

# -c writes the CIGAR the view draws insertions and deletions from
# --eqx splits the CIGAR's matches from its mismatches
# asm20 tolerates the divergence between paralogous amylase copies, so a chain
#   runs through the array instead of stopping at it
minimap2 -c --eqx -x asm20 HG00232.1.fa NA18608.2.fa |
  # tp:A:P is the pair's primary chain; the secondary ones are amylase copies
  # aligning to each other
  awk -F'\t' '$11>=5000 && /tp:A:P/' > adjacent.regions.paf

The records come out in the coordinates of the fetched pieces. The script adds each region's start back on and writes each contig's full length from the assembly's .fai, so the PAF names whole contigs and the rows draw on the assemblies' own coordinates, under gene tracks made for them.

The track

One SyntenyTrack backs every band of the stack. The PAF names its sequences PanSN-style, HG00232#1#<contig>, and assemblyNameToPanSN maps each JBrowse assembly to its prefix, so the adapter hands a band the records joining its two rows:

Config file

{
  "type": "SyntenyTrack",
  "trackId": "amylase_adjacent",
  "name": "Amylase locus, each haplotype against the next (minimap2)",
  "assemblyNames": ["HG01361.1", "hg38", "HG00133.1", "NA18608.2", "HG00232.1"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "amylase_adjacent.paf",
    "assemblyNames": [
      "HG01361.1",
      "hg38",
      "HG00133.1",
      "NA18608.2",
      "HG00232.1"
    ],
    "assemblyNameToPanSN": {
      "HG01361.1": "HG01361#1",
      "hg38": "GRCh38#0",
      "HG00133.1": "HG00133#1",
      "NA18608.2": "NA18608#2",
      "HG00232.1": "HG00232#1"
    }
  }
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "amylase_adjacent",
  "name": "Amylase locus, each haplotype against the next (minimap2)",
  "assemblyNames": ["HG01361.1", "hg38", "HG00133.1", "NA18608.2", "HG00232.1"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "amylase_adjacent.paf",
    "assemblyNames": [
      "HG01361.1",
      "hg38",
      "HG00133.1",
      "NA18608.2",
      "HG00232.1"
    ],
    "assemblyNameToPanSN": {
      "HG01361.1": "HG01361#1",
      "hg38": "GRCh38#0",
      "HG00133.1": "HG00133#1",
      "NA18608.2": "NA18608#2",
      "HG00232.1": "HG00232#1"
    }
  }
}'

JBrowse Desktop

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": "SyntenyTrack",
  "trackId": "amylase_adjacent",
  "name": "Amylase locus, each haplotype against the next (minimap2)",
  "assemblyNames": ["HG01361.1", "hg38", "HG00133.1", "NA18608.2", "HG00232.1"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "amylase_adjacent.paf",
    "assemblyNames": [
      "HG01361.1",
      "hg38",
      "HG00133.1",
      "NA18608.2",
      "HG00232.1"
    ],
    "assemblyNameToPanSN": {
      "HG01361.1": "HG01361#1",
      "hg38": "GRCh38#0",
      "HG00133.1": "HG00133#1",
      "NA18608.2": "NA18608#2",
      "HG00232.1": "HG00232#1"
    }
  }
}

amylase_adjacent.paf is relative to a config.json. Replace it with its URL or its path on this computer.

One copy to seven, each against the next

The session opens the five rows in copy-number order, each on its own contig with its own gene track, colored by strand:

Config file

{
  "defaultSession": {
    "name": "Amylase haplotypes from one AMY1 copy to seven, each aligned to the next",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          {
            "assembly": "HG01361.1",
            "loc": "CM089019.1:103,831,655-104,050,048",
            "tracks": ["hprc_genes_HG01361_1"]
          },
          {
            "assembly": "hg38",
            "loc": "chr1:103,520,894-103,832,637",
            "tracks": ["hg38_ncbiRefSeq_ucsc"]
          },
          {
            "assembly": "HG00133.1",
            "loc": "CM090045.1:103,669,666-103,981,330",
            "tracks": ["hprc_genes_HG00133_1"]
          },
          {
            "assembly": "NA18608.2",
            "loc": "CM089849.1:103,796,766-104,203,421",
            "tracks": ["hprc_genes_NA18608_2"]
          },
          {
            "assembly": "HG00232.1",
            "loc": "CM089991.1:103,491,008-103,991,760",
            "tracks": ["hprc_genes_HG00232_1"]
          }
        ],
        "tracks": [
          ["amylase_adjacent"],
          ["amylase_adjacent"],
          ["amylase_adjacent"],
          ["amylase_adjacent"]
        ],
        "colorBy": { "field": "strand" },
        "drawCurves": true,
        "levelHeights": [110, 110, 110, 110]
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "Amylase haplotypes from one AMY1 copy to seven, each aligned to the next",
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "HG01361.1",
          "loc": "CM089019.1:103,831,655-104,050,048",
          "tracks": ["hprc_genes_HG01361_1"]
        },
        {
          "assembly": "hg38",
          "loc": "chr1:103,520,894-103,832,637",
          "tracks": ["hg38_ncbiRefSeq_ucsc"]
        },
        {
          "assembly": "HG00133.1",
          "loc": "CM090045.1:103,669,666-103,981,330",
          "tracks": ["hprc_genes_HG00133_1"]
        },
        {
          "assembly": "NA18608.2",
          "loc": "CM089849.1:103,796,766-104,203,421",
          "tracks": ["hprc_genes_NA18608_2"]
        },
        {
          "assembly": "HG00232.1",
          "loc": "CM089991.1:103,491,008-103,991,760",
          "tracks": ["hprc_genes_HG00232_1"]
        }
      ],
      "tracks": [
        ["amylase_adjacent"],
        ["amylase_adjacent"],
        ["amylase_adjacent"],
        ["amylase_adjacent"]
      ],
      "colorBy": { "field": "strand" },
      "drawCurves": true,
      "levelHeights": [110, 110, 110, 110]
    }
  ]
}
EOF

URL

Open this session in JBrowse

The second band joins GRCh38 to another three-copy haplotype and runs straight across the locus, with one inverted match where the array's two oppositely oriented AMY1 copies align to each other. The first band joins one copy to three and the third joins three to five, and each opens a single wedge on the side with more copies, over two of its AMY1 genes. In the fourth band, five copies to seven, the two arrays match up in more than one way: a forward alignment covers each end, an inverted one crosses between them, and a stretch of the seven-copy row is left to no forward alignment.

One haplotype of each common amylase structure, from one AMY1 copy at the top to seven at the bottom, each with its own gene track and each aligned to the row under it, colored by strand. The two three-copy rows align straight through. One copy to three and three to five each open a wedge over the genes only the longer row carries. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Check it against the PAF

Each wedge is one CIGAR operation, so the file states its size. Print the largest insertion or deletion of each record:

python3 - <<'EOF'
import re
for line in open('amylase_adjacent.paf'):
    f = line.rstrip('\n').split('\t')
    cigar = next(t for t in f[12:] if t.startswith('cg:Z:'))
    ops = [(int(n), op) for n, op in re.findall(r'(\d+)([ID])', cigar)]
    print(f[0].split('#')[0], f[5].split('#')[0], f[4], max(ops))
EOF

The HG01361 to GRCh38 record and the HG00133 to NA18608 record each hold a deletion of 94,138 bp, the step between the span classes. No record of the GRCh38 to HG00133 band holds an operation past 838 bp, and none of the NA18608 to HG00232 band does either, since there the step falls between records.

The gene counts behind the row order come from sequence too. A lifted annotation can miss a copy the reference does not have, so GRCh38's copy of each gene is aligned to a row and every full-length hit counted:

# -N keeps that many secondary hits, which is what the extra copies are
# -p 0.5 lets a copy scoring half of the best one through
minimap2 -c --eqx -x asm20 -N 50 -p 0.5 HG00232.1.fa genes.fa |
  # a copy is a hit over 90% of the gene at 97% identity or better
  awk -F'\t' '($4-$3)/$2>=0.9 && $10/$11>=0.97 { c[$1]++ }
    END { for (g in c) print g, c[g] }'

Row	AMY1	AMY2A	AMY2B
HG01361.1	1	1	1
GRCh38	3	1	1
HG00133.1	3	1	1
NA18608.2	5	1	1
HG00232.1	7	1	1

GRCh38 comes back with the three AMY1 copies it is annotated with.

Pair alignments read off the graph

The HPRC graph already aligns every haplotype to every other: two walks through one node carry the same bases. At a locus the graph resolves, a stack needs no FASTA and no aligner. The complement C4 locus is one. A haplotype carries one to four copies of a 32.7 kb module, and the C4 gene in each copy is long or short by a 6.4 kb HERV-K insertion (Sekar et al. 2016).

gbz-base-query reads the window out of the graph database once and writes each row against the row under it, on each haplotype's own coordinates:

GBZ_DB=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.gbz.db
GBZ_INDEX=https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.anchored.db
# --stack lists the rows from the top, and each is aligned to the next: a node
#   both walks visit becomes a run of =, and the bases between two shared nodes
#   are aligned into =, X, I and D, so a module-sized insertion stays inside
#   one record, where the view draws it from the CIGAR
# --contig-lengths fills the PAF's two length columns, which a window of the
#   graph does not hold
npx --yes -p @gmod/gbz-base gbz-base-query $GBZ_DB --haplotype-index $GBZ_INDEX \
  --sample GRCh38 --contig chr6 --interval 31940000..32090000 --context 0 \
  --stack 'HG01978#2,HG02004#2,GRCh38#0,HG02818#1,HG00146#1' \
  --contig-lengths contig_lengths.tsv > adjacent.paf

The rows are two haplotypes with three modules, GRCh38 with two, HG02818.1 with two and a short C4B, and HG00146.1 with one:

Config file

{
  "defaultSession": {
    "name": "C4 haplotypes, each against the next, from the graph",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          {
            "assembly": "HG01978.2",
            "loc": "CM089273.1:31,872,045-32,055,037",
            "tracks": ["hprc_genes_HG01978_2"]
          },
          {
            "assembly": "HG02004.2",
            "loc": "JBHDRU010000054.1:31,876,435-32,059,471",
            "tracks": ["hprc_genes_HG02004_2"]
          },
          {
            "assembly": "hg38",
            "loc": "chr6:31,939,722-32,090,034",
            "tracks": ["hg38_ncbiRefSeq_ucsc"]
          },
          {
            "assembly": "HG02818.1",
            "loc": "JAHEOS020000050.1:31,980,558-32,124,509",
            "tracks": ["hprc_genes_HG02818_1"]
          },
          {
            "assembly": "HG00146.1",
            "loc": "CM090015.1:31,912,959-32,024,178",
            "tracks": ["hprc_genes_HG00146_1"]
          }
        ],
        "tracks": [
          ["graph_adjacent"],
          ["graph_adjacent"],
          ["graph_adjacent"],
          ["graph_adjacent"]
        ],
        "colorBy": { "field": "strand" },
        "drawCurves": true,
        "levelHeights": [110, 110, 110, 110]
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "C4 haplotypes, each against the next, from the graph",
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "HG01978.2",
          "loc": "CM089273.1:31,872,045-32,055,037",
          "tracks": ["hprc_genes_HG01978_2"]
        },
        {
          "assembly": "HG02004.2",
          "loc": "JBHDRU010000054.1:31,876,435-32,059,471",
          "tracks": ["hprc_genes_HG02004_2"]
        },
        {
          "assembly": "hg38",
          "loc": "chr6:31,939,722-32,090,034",
          "tracks": ["hg38_ncbiRefSeq_ucsc"]
        },
        {
          "assembly": "HG02818.1",
          "loc": "JAHEOS020000050.1:31,980,558-32,124,509",
          "tracks": ["hprc_genes_HG02818_1"]
        },
        {
          "assembly": "HG00146.1",
          "loc": "CM090015.1:31,912,959-32,024,178",
          "tracks": ["hprc_genes_HG00146_1"]
        }
      ],
      "tracks": [
        ["graph_adjacent"],
        ["graph_adjacent"],
        ["graph_adjacent"],
        ["graph_adjacent"]
      ],
      "colorBy": { "field": "strand" },
      "drawCurves": true,
      "levelHeights": [110, 110, 110, 110]
    }
  ]
}
EOF

URL

Open this session in JBrowse

Five haplotypes across C4, each with its own gene track and each aligned to the row under it off the graph's walks. The two three-module rows at the top align straight through. Below them the wedges are the module GRCh38 lacks, the HERV-K insertion inside GRCh38's C4B, and, in two pieces, the module the one-module row lacks. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The top band runs through a module GRCh38 does not have. Open the same track in HG02004.2's own view at JBHDRU010000054.1:31,942,330-31,942,580, inside that module, where a synteny track draws each aligned haplotype as a row:

The synteny track in HG02004.2's own view, inside the module GRCh38 lacks. The HG01978.2 row marks each substituted base, insertion and deletion; the hg38 row is one deletion across the whole window. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The check above on adjacent.paf prints the module as one 32,738 bp insertion and the HERV-K as 6,367 bp. The last record holds the same module as a short one and its HERV-K, 26,370 and 6,368 bp.

The script wraps the command and writes the config. REGION and ROWS pick the window and the stack, so the amylase rows from the top of the page go through it as well. There the graph folds the paralogous copies onto shared nodes, and the rows are aligned by comparing their bases through the array.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_graph_haplotype_stack.sh
# REGION is on GRCh38; ROWS is the stack from the top, GRCh38#0 for the reference
REGION=chr6:31940000-32090000 \
  ROWS='HG01978#2 HG02004#2 GRCh38#0 HG02818#1 HG00146#1' \
  bash build_graph_haplotype_stack.sh
# the amylase stack:
#   REGION=chr1:103539800-103801379
#   ROWS='HG01361#1 GRCh38#0 HG00133#1 NA18608#2 HG00232#1'

Reproduce it end to end

The script reads the two windows from the graph database, fetches the five regions, aligns the four adjacent pairs, lifts the records onto whole contigs, counts the genes and writes the config; see Prerequisites. Its manifest is one row per haplotype, the assembly name, the contig's PanSN name, a FASTA and a region, and the row order is the stack order, so another locus or another set of haplotypes is an edit to that table. locus_spans.tsv lists every haplotype's span, to pick other rows from.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_amylase_haplotypes.sh
bash build_amylase_haplotypes.sh

References

Sekar A, et al. Schizophrenia risk from complex variation of complement component 4. Nature (2016). https://doi.org/10.1038/nature16549
Yilmaz F, et al. Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation. Science (2024). https://doi.org/10.1126/science.adn0609
Bolognini D, et al. Recurrent evolution and selection shape structural diversity at the amylase locus. Nature (2024). https://doi.org/10.1038/s41586-024-07911-1
Usher CL, et al. Structural forms of the human amylase locus and their relationships to SNPs, haplotypes and obesity. Nat Genet (2015). https://doi.org/10.1038/ng.3340
HPRC release 2, the release whose graph, assemblies and CAT annotations this page reads.
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics (2018). https://doi.org/10.1093/bioinformatics/bty191

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Synteny between neighbouring haplotypes (the amylase locus)

Prerequisites#

Where the data comes from#

The locus under GRCh38 alone#

A haplotype of each structure#

Aligning each haplotype to its neighbour#

The track#

One copy to seven, each against the next#

Check it against the PAF#

Pair alignments read off the graph#

Reproduce it end to end#

See also#

References#

Prerequisites

Where the data comes from

The locus under GRCh38 alone

A haplotype of each structure

Aligning each haplotype to its neighbour

The track

One copy to seven, each against the next

Check it against the PAF

Pair alignments read off the graph

Reproduce it end to end

See also

References