JBrowse2：1000Genomes可视化

项目结构：

html：

<h1>We're using JBrowse Linear View!</h1>
<div>
<div id="jbrowse_linear_view" style="min-height:700px;"></div>
<script type="module" src="../static/js/jbrowse/assemblymanage.js" ></script>
</div>

assemblymanage.js:

import * as genome from './assembly.js'

var variant_tracks = new Array()

//chr22
import * as chr22_tracks from './chr22_tracks.js'
variant_tracks['chr22'] = chr22_tracks
variant_tracks['chr22_seq']=genome.chr22

//初始界面设定
var tracks = variant_tracks['chr22'].tracks
var assembly = variant_tracks['chr22_seq']
var genomeView = new JBrowseLinearGenomeView({
    container: document.getElementById('jbrowse_linear_view'),
    assembly,
    tracks
    // location: '22:10,210..21,798',
})

assembly.js:（uri地址错误，可下载放在项目里）

export var chr22 = {
    name:"chr22",
        sequence:{
            type:'ReferenceSequenceTrack',
            trackId:'chr22_ReferenceSequenceTrack',
            adapter:{
                type: 'BgzipFastaAdapter',
                fastaLocation: {
                    uri: "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
                },
                faiLocation: {
                    uri: "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz.fai"
                },
                gziLocation: {
                    uri: "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz.gzi"
                }
            }
        }
}

chr22_tracks.js:（目前只展示chr22）

export var tracks = [
    {
        type:'VariantTrack',
        trackId:'ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf',
        name:"1000 Genomes Variant Calls CHR",
        category:['1000Genomes','Variants'],
        assemblyNames:['chr22'],
        adapter:{
            type: 'VcfTabixAdapter',
            vcfGzLocation:{
                uri:
                    '../static/data/chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz',
            },
            index:{
                location:{
                    uri:
                        '../static/data/chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz.tbi',
                },
                indexType:'TBI',
            }
        }
    }
]

页面效果图：

待续…