Human structural variants (hg19)

Browse HG002 PacBio breakend structural variants on hg19, LocusZoom-style circular layout.

HG002 PacBio structural-variant calls on hg19 — a breakend-only VCF from GIAB, opened on first paint. The VCF is fetched over HTTP range requests, so there is no server-side component, and chromosome-spanning breakends render as chords across the circle.

For the surrounding setup see the minimal example; for the config slots, VcfTabixAdapter and VariantTrack.

View source — 34 lines

import { CircularGenomeView } from '@jbrowse/react-circular-genome-view2'

const assembly = {
  name: 'hg19',
  aliases: ['GRCh37'],
  uri: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz',
  refNameAliases: {
    uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg19_aliases.txt',
  },
}

const tracks = [
  {
    type: 'VariantTrack',
    trackId: 'pacbio_sv_vcf',
    name: 'HG002 Pacbio SV (VCF)',
    assemblyNames: ['hg19'],
    category: ['GIAB'],
    adapter: {
      type: 'VcfTabixAdapter',
      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf.gz',
    },
  },
]

export default function Human() {
  return (
    <CircularGenomeView
      assembly={assembly}
      tracks={tracks}
      init={{ tracks: ['pacbio_sv_vcf'] }}
    />
  )
}