Variant Track

The variant track (type="variant") displays variant records from "VCF" files or equivalents.

File formats#

• vcf

Configuration Options#

General options

Property	Description	Default
displayMode	Display option. 'COLLAPSED' => show variants only, 'SQUISHED' and 'EXPANDED' => show calls.	'EXPANDED'
squishedCallHeight	Height of genotype call rows in SQUISHED mode.	1
expandedCallHeight	Height of genotype call rows in EXPANDED mode	10

Variant color options#

Property	Description	Default
color	Specify a variant color, or function that takes a variant object and returns a color.
colorBy	Specify an INFO field to color variants by. Optional, if specified takes precedence over color property
colorTable	Color table mapping INFO field values to colors. Use in conjunction with colorBy. Optional, if not specified a color table will be generated.

Genotype color options#

Property	Description	Default
noCallColor	Color for no-calls	"rgb(250, 250, 250)"
homvarColor	CSS color for homozygous non-reference calls.	"rgb(17,248,254)"
hetvarColor	CSS color for heterozygous calls.	"rgb(34,12,253)"
homrefColor	CSS color for homozygous reference calls.	"rgb(200, 200, 200)"

Examples#

Tabix indexed file#

{
  type: "variant",
  format: "vcf",
  url: "https://s3.amazonaws.com/1000genomes/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz",
  indexURL: "https://s3.amazonaws.com/1000genomes/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi",
  name: "1KG variants (chr22)",
  squishedCallHeight: 1,
  expandedCallHeight: 4,
  displayMode: "squished",
  visibilityWindow: 1000
}

 ```

### Color-by info field with color table

```javascript
{
    url: "https://s3.amazonaws.com/igv.org.demo/nstd186.GRCh38.variant_call.vcf.gz",
    indexURL: "https://s3.amazonaws.com/igv.org.demo/nstd186.GRCh38.variant_call.vcf.gz.tbi",
    name: "Color by table, SVTYPE",
    visibilityWindow: -1,
    colorBy: "SVTYPE",
    colorTable: {
        "DEL": "#ff2101",
        "INS": "#001888",
        "DUP": "#028401",
        "INV": "#008688",
        "CNV": "#8931ff",
        "BND": "#891100",
        "*": "#002eff"
     }
}

Color-by function. NOTE: functions cannot be saved in session files.#

{
    url: "https://s3.amazonaws.com/igv.org.demo/nstd186.GRCh38.variant_call.vcf.gz",
    indexURL: "https://s3.amazonaws.com/igv.org.demo/nstd186.GRCh38.variant_call.vcf.gz.tbi",
    name: "Color by function, SVTYPE",
    visibilityWindow: -1,
    color: function (variant) {
        const svtype = variant.info["SVTYPE"];
        switch (svtype) {
            case 'DEL':
                return "#ff2101";
            case 'INS':
                return "#001888";
            case 'DUP':
                return "#028401";
            case 'INV':
                return "#008688";
            case 'CNV':
                return "#8931ff";
            case 'BND':
                return "#891100";
             default:
                return "#002eff";
         }
     }
}