Inspecting phased reads (GIAB HG002)

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.17. Desktop beta builds are coming soon.

HG002 is the Genome in a Bottle (GIAB) Ashkenazi son, a human benchmark sample. GIAB publishes reads of HG002 from every major platform, and the long reads carry an HP tag from WhatsHap saying which parental haplotype each read came from. We:

open HG002 Oxford Nanopore, PacBio and Illumina reads beside the GIAB SV benchmark
group and color the nanopore reads by HP, so a heterozygous deletion sits in one haplotype's section
compare one insertion across the three platforms
split coverage by strand to separate a real variant from a basecalling artifact
color reads by 5mC and group them by HP at an imprinted CpG island

Prerequisites

the JBrowse demo, whose GIAB category in the track selector holds every track below, or your own instance with hg19 loaded (assemblies guide)

The data

GIAB's HG002 reads over two hg19 chr1 windows (1:55.69-55.72Mb and 1:62.99-63.02Mb), plus the GIAB Tier 1 SV benchmark. Nothing to download: the demo tracks read slices of these files by URL.

Read by URL (no download needed)

What it is	File
HG002 reads from every GIAB platform, the full genomes	HG002_NA24385_son/
GIAB Tier 1 SV benchmark v0.6, read by the SV track	HG002_SVs_Tier1_v0.6.vcf.gz

Loading phased reads

On your own instance, a haplotagged BAM loads like any other alignments track. The facet setting opens the track already split by HP:

Config file

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

{
  "type": "AlignmentsTrack",
  "trackId": "hg002_ont_hp",
  "name": "HG002 ONT, phased",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BamAdapter",
    "bamLocation": {
      "uri": "https://jbrowse.org/demos/hg002/HG002.ONTrel2.HP.hs37d5.demo_slices.bam"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/hg002/HG002.ONTrel2.HP.hs37d5.demo_slices.bam.bai"
      }
    }
  },
  "displayDefaults": {
    "facet": { "field": "tags.HP" },
    "encoding": { "color": "tags.HP" }
  }
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "AlignmentsTrack",
  "trackId": "hg002_ont_hp",
  "name": "HG002 ONT, phased",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BamAdapter",
    "bamLocation": {
      "uri": "https://jbrowse.org/demos/hg002/HG002.ONTrel2.HP.hs37d5.demo_slices.bam"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/hg002/HG002.ONTrel2.HP.hs37d5.demo_slices.bam.bai"
      }
    }
  },
  "displayDefaults": {
    "facet": { "field": "tags.HP" },
    "encoding": { "color": "tags.HP" }
  }
}'

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": "AlignmentsTrack",
  "trackId": "hg002_ont_hp",
  "name": "HG002 ONT, phased",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BamAdapter",
    "bamLocation": {
      "uri": "https://jbrowse.org/demos/hg002/HG002.ONTrel2.HP.hs37d5.demo_slices.bam"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/hg002/HG002.ONTrel2.HP.hs37d5.demo_slices.bam.bai"
      }
    }
  },
  "displayDefaults": {
    "facet": { "field": "tags.HP" },
    "encoding": { "color": "tags.HP" }
  }
}

A heterozygous deletion in one haplotype

Navigate to 1:63,005,000-63,008,000 and open HG002 BAM ultralong nanopore+whatshap. From the track menu, Group by... → Tag... asks for the tag name and lists the values it finds in view:

Group by... → Tag... with HP typed as the tag.

Grouped by HP and colored by the same tag, the pileup splits into one section per haplotype, plus a section for untagged reads. The deletion from the GIAB SV track shows as a gap in one section only:

HG002 nanopore reads grouped by HP tag under the GIAB SV benchmark track.

The alignments guide covers grouping by any tag, collapsing sections, and the matching sort and filter options.

One insertion across three platforms

Navigate to 1:55,705,770-55,706,090 and open the nanopore, PacBio and Illumina tracks together. JBrowse draws the insertion inside each long read as a purple mark. The 250 bp Illumina reads stop at its edges, and Show... → Soft clipping draws the unaligned bases they carry past them:

HG002 nanopore, PacBio and Illumina reads over one insertion, soft clipping shown on the Illumina track.

Strand-split coverage

Mismatch columns that come from basecalling errors often show on one strand only. Group by... → Strand on the nanopore track gives each section a coverage band built from its own reads:

HG002 nanopore reads grouped by strand. The left box disagrees in the reverse band only, the right box in both.

Methylation by haplotype

HG002's nanopore reads also carry 5mC calls in their MM/ML tags. On hg38, navigate to the SNRPN imprinting center at chr15:24,948,000-24,962,000 and open HG002 ONT reads (5mC, haplotagged). Color by... → Per-base coloring → Modifications paints each CpG from its 5mC call, and Group by... → Tag... with HP puts the methylated parental allele in one section and the unmethylated one in the other:

HG002 ONT reads over the SNRPN CpG island colored by 5mC. Top: file order. Bottom: grouped by the HP tag.

Inspecting phased reads (GIAB HG002)

Prerequisites#

The data#

Loading phased reads#

A heterozygous deletion in one haplotype#

One insertion across three platforms#

Strand-split coverage#

Methylation by haplotype#

See also#