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htsget_interop.html
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htsget_interop.html
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<!DOCTYPE html>
<!--
View this page live at one of these locations:
http://samtools.github.io/hts-specs/htsget_interop.html
https://cdn.rawgit.com/samtools/hts-specs/master/htsget_interop.html
-->
<html lang="en">
<head>
<title>htsget interop</title>
<link rel="stylesheet" href="https://www.ga4gh.org/wp-content/themes/ga4gh-theme/style.css" />
<script src="https://unpkg.com/clipboard@1.7.1/dist/clipboard.min.js"></script>
<script language="javascript">
var datasets = {
NA12878_b37: { nm: "NA12878 WGS", ref: "b37", fmts: ["BAM"] },
NA12878_hg38: { nm: "NA12878 WGS", ref: "hg38", fmts: ["CRAM"] },
NA12891_b37: { nm: "NA12891 WGS", ref: "b37", fmts: ["BAM"] },
NA12891_hg38: { nm: "NA12891 WGS", ref: "hg38", fmts: ["CRAM"] },
NA12892_b37: { nm: "NA12892 WGS", ref: "b37", fmts: ["BAM"] },
NA12892_hg38: { nm: "NA12892 WGS", ref: "hg38", fmts: ["CRAM"] },
ENCFF284YOU: { nm: "ENCFF284YOU RNA-seq", ref: "hg38", fmts: ["BAM"] },
ENCFF000VWO: { nm: "ENCFF000VWO ChIP-seq", ref: "hg38", fmts: ["BAM"] }
};
var endpoints = {
Sanger: {
nm: "Sanger",
datasets: {
NA12878_b37: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/NA12878" },
NA12878_hg38: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/NA12878_GRCH38" },
NA12891_b37: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/NA12891" },
NA12891_hg38: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/NA12891_GRCH38" },
NA12892_b37: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/NA12892" },
NA12892_hg38: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/NA12892_GRCH38" },
ENCFF284YOU: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/ENCFF284YOU_GRCH38" },
ENCFF000VWO: { url: "https://htsget.wtsi-npg-test.co.uk:9090/npg_ranger/ga4gh/sample/ENCFF000VWO" }
}
},
DNAnexus_AWS: {
nm: "DNAx/AWS",
datasets: {
NA12878_b37: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12878" },
NA12878_hg38: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_hg38/NA12878" },
NA12891_b37: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12891" },
NA12891_hg38: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_hg38/NA12891" },
NA12892_b37: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12892" },
NA12892_hg38: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_hg38/NA12892" },
ENCFF284YOU: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/ENCODE/ENCFF284YOU" },
ENCFF000VWO: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/ENCODE/ENCFF000VWO" }
}
},
DNAnexus_Azure: {
nm: "DNAx/Azure",
datasets: {
NA12878_b37: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_BroadHiSeqX_b37/NA12878" },
NA12878_hg38: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_BroadHiSeqX_hg38/NA12878" },
NA12891_b37: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_BroadHiSeqX_b37/NA12891" },
NA12891_hg38: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_BroadHiSeqX_hg38/NA12891" },
NA12892_b37: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_BroadHiSeqX_b37/NA12892" },
NA12892_hg38: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_BroadHiSeqX_hg38/NA12892" },
ENCFF284YOU: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_ENCODE/ENCFF284YOU" },
ENCFF000VWO: { url: "https://htsnexus.rnd.dnanex.us/v1/reads/Azure_ENCODE/ENCFF000VWO" }
}
},
Google: {
nm: "Google",
datasets: {
NA12878_b37: { url: "http://35.196.212.220/reads/ga4gh-demo-public/NA12878.bam" },
NA12891_b37: { url: "http://35.196.212.220/reads/ga4gh-demo-public/NA12891.bam" },
NA12892_b37: { url: "http://35.196.212.220/reads/ga4gh-demo-public/NA12892.bam" },
ENCFF284YOU: { url: "http://35.196.212.220/reads/ga4gh-demo-public/ENCFF284YOU.bam" },
ENCFF000VWO: { url: "http://35.196.212.220/reads/ga4gh-demo-public/ENCFF000VWO.bam" }
}
}
};
var exampleRange = {
hg38: "referenceName=chr12&start=111766922&end=111817529",
b37: "referenceName=12&start=112204691&end=112247789"
};
var exampleRangeName = "ALDH2";
</script>
</head>
<body>
<div class="hero-l">
<div class="hero-box">
<div class="hero-title">
<h3>htsget interop</h3>
</div>
<div class="hero-line"><hr /></div>
<div class="hero-txt">
<p>Table of htsget endpoints for interoperability testing, with test data including a WGS trio contributed by the Broad Inst with NHGRI support (1UM1HG008895-01), and functional genomics runs from <a href="https://www.encodeproject.org/">ENCODE</a>.</p>
</p>
</div>
</div>
</div>
<div class="landing-article">
<div class="page-margin">
<div id="interopTable">
</div>
<p>Click a link above to show a <a href="https://github.com/samtools/samtools/releases">samtools 1.7+</a> invocation to slice an example region, using the respective endpoint. Add <tt>-b</tt> to make samtools emit BAM instead of SAM.</p>
<textarea rows="3" cols="100" id="exampleCommand" onfocus="this.select();" style="font-family: courier">The quick brown fox jumps over the lazy dog.</textarea>
<button class="clip" data-clipboard-target="#exampleCommand">📋 Copy</button>
<br/><br/>
<a href="https://github.com/samtools/hts-specs/blob/master/htsget_interop.html">View source on GitHub</a>
<script language="javascript">
function updateExample() {
var box = document.getElementById("exampleCommand");
var d = endpoints[this.info.endpoint].datasets[this.info.dataset];
var formats = d.fmts ? d.fmts : datasets[this.info.dataset].fmts;
var url = d.url + "?" + exampleRange[datasets[this.info.dataset].ref];
if (formats.indexOf('CRAM') >= 0) {
url += "&format=CRAM";
}
box.innerText = 'samtools view -h "' + url + '" > ' + this.info.dataset + "_" + exampleRangeName + '.sam';
return false;
}
var div = document.getElementById("interopTable");
var table = document.createElement("table");
var first = true;
for (var dataset in datasets) {
var tr = table.insertRow();
var td = tr.insertCell();
td.appendChild(document.createTextNode(datasets[dataset].nm + ' (' + datasets[dataset].ref + ')'));
for (var endpoint in endpoints) {
td = tr.insertCell();
if (endpoints[endpoint].datasets[dataset]) {
var a = document.createElement("a");
a.href = "#";
a.appendChild(document.createTextNode(endpoints[endpoint].nm));
a.info = {
endpoint: endpoint,
dataset: dataset
};
a.onclick = updateExample;
td.appendChild(a);
if (first) {
first = false;
updateExample.apply(a);
}
}
}
}
div.appendChild(table);
var cb = new Clipboard('.clip');
</script>
</div>
</div>
</body>
</html>