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test.html
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test.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no">
<meta name="description" content="">
<meta name="author" content="">
<link rel="shortcut icon" href="img/favicon.ico">
<title>igv.js</title>
<!-- IGV JS-->
<script src="dist/igv.js"></script>
<style>
#trackList {
border-color: rgb(127, 127, 127);
border-style: solid;
border-width: thin;
width: 480px;
height: 256px;
overflow-y: auto;
}
div#trackList > div, div#myDiv > h3 {
font-family: 'PT Sans', sans-serif;
font-size: small;
font-weight: 400;
color: #444;
margin-left: 16px;
margin-top: 4px;
margin-bottom: 4px;
padding-left: 32px;
}
div#myDiv > h3 {
font-size: large;
}
div#trackList > div:hover,
div#trackList > div:focus,
div#trackList > div:active {
cursor: pointer;
color: white;
background-color: rgba(49, 106, 246, 1);
}
</style>
</head>
<body>
<p>
<h1>igv.js test page</h1>
<h3>Example tracks - click to load</h3>
<div id="trackList">
<div onclick="igv.browser.loadTrack({
url: 'https://s3-us-west-2.amazonaws.com/ilmn.igv-test/test2.bigWig',
min: 1,
name: 'Big BigWig'
})"> Big BigWig
</div>
<div onclick="igv.browser.loadTrack({
url: 'https://data.broadinstitute.org/igvdata/1KG/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz',
indexURL: 'https://data.broadinstitute.org/igvdata/1KG/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi',
visibilityWindow: 20000,
name: '1KG Sites'
})">VCF file (1KG sites)
</div>
<div onclick="igv.browser.loadTrack({
type: 'variant',
url: 'https://s3.amazonaws.com/igv.broadinstitute.org/data/hg19/1kg/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz',
name: '1KG variants',
visibilityWindow: 1000
})">VCF file with genotypes (chr 22)
</div>
<div onclick="igv.browser.loadTrack({
sourceType: 'gcs',
type: 'bam',
url: 'gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam',
height: 500,
autoHeight: false,
viewAsPairs: true,
name: 'NA12877'})">Google Cloud Storage - NA12877_S1.bam
</div>
<div onclick="igv.browser.loadTrack({
sourceType: 'ga4gh',
type: 'bam',
url: 'https://genomics.googleapis.com/v1',
readGroupSetIds: 'CMvnhpKTFhCjz9_25e_lCw',
height: 200,
autoHeight: false,
name: 'Ga4gh alignments'})">GA4Gh Alignments (Global Alliance, Google server)
</div>
<div onclick="igv.browser.loadTrack({
sourceType: 'ga4gh',
type: 'vcf',
url: 'https://genomics.googleapis.com/v1',
variantSetId: '10473108253681171589',
visibilityWindow: 10000,
name: 'Ga4gh variants'
})">GA4Gh Variants (Global Alliance, Google server)
</div>
<div onclick="igv.browser.loadTrack({
sourceType: 'ga4gh',
type: 'variant',
url: 'https://genomics.googleapis.com/v1',
variantSetId: ['10473108253681171589'],
callSetIds: ['10473108253681171589-2'],
visibilityWindow: 100000,
name: 'Ga4gh variants'
})">GA4Gh Variants - 1 callset (Global Alliance, Google server)
</div>
<div onclick="igv.browser.loadTrack({
sourceType: 'ga4gh',
type: 'variant',
url: 'https://genomics.googleapis.com/v1',
variantSetId: ['10473108253681171589'],
includeCalls: false,
visibilityWindow: 100000,
name: 'Ga4gh variants'
})">GA4Gh Variants - NO callsets (Global Alliance, Google server)
</div>
<div onclick="igv.browser.loadTrack({
url: 'https://data.broadinstitute.org/igvdata/test/igv-web/segmented_data_080520.seg.gz',
indexed: false,
isLog: true,
name: 'GBM Copy # (TCGA Broad GDAC)'})">GBM Copy # (TCGA Broad GDAC)) (SEG)
</div>
<div onclick="igv.browser.loadTrack({
url: 'https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.collapsed.bed.gz',
name: 'gencode'
})"> gencode collapsed (tabix)
</div>
<div onclick="igv.browser.loadTrack({
type: 'bed',
url: 'https://data.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz',
name: 'dbSNP 137',
visibilityWindow: 200000
})">dbSNP 137 (bed tabix)
</div>
<div onclick="igv.browser.loadTrack({
url: 'https://www.encodeproject.org/files/ENCFF002ADR/@@download/ENCFF002ADR.bigBed',
name: 'ENCFF002ADR',
visibilityWindow: 2000000,
height: 50,
autoHeight: false
})">Encode bigbed
</div>
<div onclick="igv.browser.loadTrack({
url: 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me3StdSig.bigWig',
name: 'Gm12878H3k4me3'
})">Encode bigwig
</div>
<div onclick="igv.browser.loadTrack({
url: 'https://data.broadinstitute.org/igvdata/encode/hg19/broadHistone/wgEncodeBroadHistoneGm12878H3k4me2StdSig.wig.tdf',
name: 'GM12878H3k4m3 (tdf)'
})">Broad tdf
</div>
<div onclick="igv.browser.loadTrack({
url: 'https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v24lift37.annotation.sorted.gtf.gz',
indexURL: 'https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v24lift37.annotation.sorted.gtf.gz.tbi',
name: 'Gencode v24',
format: 'gtf',
visibilityWindow: 10000000
})">Gencode v24 gtf (tabix indexed)
</div>
<div onclick="igv.browser.loadTrack({
type: 'eqtl',
sourceType: 'gtex-ws',
url: 'https://dev.gtexportal.org/rest/v1/association/singleTissueEqtlByLocation',
tissueName: 'Adipose_Subcutaneous',
name: 'Adipose - Subcutaneous',
visibilityWindow: 1000000
})">Adipose - Subcutaneous
</div>
</div>
<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"/>
<script type="text/javascript">
document.addEventListener("DOMContentLoaded", function () {
var div = document.getElementById("igvDiv"),
options = {
showChromosomeWidget: true,
genome: "hg19",
// locus: "all",
locus: ['myc'],
apiKey: 'AIzaSyDUUAUFpQEN4mumeMNIRWXSiTh5cPtUAD0',
tracks: [
{
url: 'http://data.broadinstitute.org/igvdata/1KG/b37/data/HG02450/alignment/HG02450.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam',
label: 'HG02450'
},
{
name: "Genes",
type: "annotation",
format: "bed",
sourceType: "file",
url: "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz",
indexURL: "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz.tbi",
order: Number.MAX_VALUE,
visibilityWindow: 300000000,
displayMode: "EXPANDED",
autoHeight: true
}
],
supportQueryParameters: true
};
igv.createBrowser(div, options);
});
</script>
</body>
</html>