snv.vcf

##fileformat=VCFv4.1
##source=VarScan2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
20	61795	.	G	T	.	PASS	DP=81;SS=1;SSC=2;GPV=4.6768E-16;SPV=5.4057E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:44:22:22:50%:16,6,9,13	0/1:.:37:18:19:51.35%:10,8,10,9
20	62731	.	C	A	.	PASS	DP=68;SS=1;SSC=1;GPV=1.4855E-11;SPV=7.5053E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:32:17:15:46.88%:9,8,9,6	0/1:.:36:21:15:41.67%:8,13,8,7
20	63799	.	C	T	.	PASS	DP=72;SS=1;SSC=7;GPV=3.6893E-16;SPV=1.8005E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:39:19:19:50%:8,11,11,8	0/1:.:33:12:21:63.64%:5,7,8,13
20	65288	.	G	T	.	PASS	DP=35;SS=1;SSC=0;GPV=7.8434E-5;SPV=8.2705E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:21:13:8:38.1%:4,9,0,8	0/1:.:14:10:4:28.57%:2,8,0,4
20	65900	.	G	A	.	PASS	DP=53;SS=1;SSC=0;GPV=1.5943E-31;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:26:0:26:100%:0,0,12,14	1/1:.:27:0:27:100%:0,0,15,12
20	66370	.	G	A	.	PASS	DP=66;SS=1;SSC=0;GPV=2.6498E-39;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:32:0:32:100%:0,0,11,21	1/1:.:34:0:34:100%:0,0,15,19
20	68749	.	T	C	.	PASS	DP=64;SS=1;SSC=0;GPV=4.1752E-38;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:23:0:23:100%:0,0,7,16	1/1:.:41:0:41:100%:0,0,21,20
20	69094	.	G	A	.	PASS	DP=25;SS=1;SSC=8;GPV=4.2836E-5;SPV=1.5657E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:12:8:4:33.33%:5,3,4,0	0/1:.:13:5:8:61.54%:3,2,6,2
20	69408	.	C	T	.	PASS	DP=53;SS=1;SSC=0;GPV=8.7266E-12;SPV=9.8064E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:27:9:18:66.67%:5,4,9,9	0/1:.:26:15:11:42.31%:6,9,4,7
20	75254	.	C	A	.	PASS	DP=74;SS=1;SSC=9;GPV=7.9203E-12;SPV=1.1567E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:34:22:11:33.33%:13,9,5,6	0/1:.:40:20:20:50%:5,15,14,6

snv2.vcf

##fileformat=VCFv4.1
##source=VarScan2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
20	61796	.	G	T	.	PASS	DP=81;SS=1;SSC=2;GPV=4.6768E-16;SPV=5.4057E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:44:22:22:50%:16,6,9,13	0/1:.:37:18:19:51.35%:10,8,10,9
20	62732	.	C	A	.	PASS	DP=68;SS=1;SSC=1;GPV=1.4855E-11;SPV=7.5053E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:32:17:15:46.88%:9,8,9,6	0/1:.:36:21:15:41.67%:8,13,8,7
20	63800	.	C	T	.	PASS	DP=72;SS=1;SSC=7;GPV=3.6893E-16;SPV=1.8005E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:39:19:19:50%:8,11,11,8	0/1:.:33:12:21:63.64%:5,7,8,13
20	65289	.	G	T	.	PASS	DP=35;SS=1;SSC=0;GPV=7.8434E-5;SPV=8.2705E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:21:13:8:38.1%:4,9,0,8	0/1:.:14:10:4:28.57%:2,8,0,4
20	65901	.	G	A	.	PASS	DP=53;SS=1;SSC=0;GPV=1.5943E-31;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:26:0:26:100%:0,0,12,14	1/1:.:27:0:27:100%:0,0,15,12
20	66371	.	G	A	.	PASS	DP=66;SS=1;SSC=0;GPV=2.6498E-39;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:32:0:32:100%:0,0,11,21	1/1:.:34:0:34:100%:0,0,15,19
20	68750	.	T	C	.	PASS	DP=64;SS=1;SSC=0;GPV=4.1752E-38;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:23:0:23:100%:0,0,7,16	1/1:.:41:0:41:100%:0,0,21,20
20	69095	.	G	A	.	PASS	DP=25;SS=1;SSC=8;GPV=4.2836E-5;SPV=1.5657E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:12:8:4:33.33%:5,3,4,0	0/1:.:13:5:8:61.54%:3,2,6,2
20	69409	.	C	T	.	PASS	DP=53;SS=1;SSC=0;GPV=8.7266E-12;SPV=9.8064E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:27:9:18:66.67%:5,4,9,9	0/1:.:26:15:11:42.31%:6,9,4,7
20	75255	.	C	A	.	PASS	DP=74;SS=1;SSC=9;GPV=7.9203E-12;SPV=1.1567E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:34:22:11:33.33%:13,9,5,6	0/1:.:40:20:20:50%:5,15,14,6

vcf2.html

<!doctype html>
<script src="//ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>

<link rel="stylesheet" href="dalliance/css/bootstrap-scoped.css" />
<link rel="stylesheet" href="dalliance/css/dalliance-scoped.css" />
<link rel="stylesheet" href="dalliance/css/font-awesome.min.css" />
<script type="text/javascript" src="dalliance/dalliance-all.js"></script>

<style>
#svgHolder {
  width: 1024px;
  height: 768px;
}
</style>

<div id="svgHolder"></div>

<script>
var vcfBytes1, vcfBytes2;
var bothLoaded = $.Deferred();
$.get('/snv.vcf', function(d) {
  vcfBytes1 = d;
  $.get('/snv2.vcf', function(d) {
    vcfBytes2 = d;
    bothLoaded.resolve();
  });
});


bothLoaded.done(function() {
  var sources = [
      {
        name: 'Genome',
        twoBitURI: 'http://www.biodalliance.org/datasets/hg19.2bit',
        tier_type: 'sequence'
      },
      {
        name: 'VCF1',
        tier_type: 'memstore',
        payload: 'vcf',
        // uri: '/snv.vcf'
        blob: new Blob([vcfBytes1])
      },
      {
        name: 'VCF2',
        tier_type: 'memstore',
        payload: 'vcf',
        // uri: '/snv2.vcf'
        blob: new Blob([vcfBytes2])
      }
  ];

  var browser = new Browser({
      chr:       '20',  // random position -- it will be changed.
      viewStart: 61770,
      viewEnd:   61820,

      // noSourceCSS: true,
      // uiPrefix: document.location.protocol + '//' + document.location.host + '/dalliance/',
      noPersist: true,

      coordSystem: {
        speciesName: 'Human',
        taxon: 9606,
        auth: 'NCBI',
        version: '37',
        ucscName: 'hg19'
      },

      sources: sources
    });
});

</script>