Tracks

Tracks in igv.js are categorized by type. Each type is designed to display a particular class of genomic data, such as read alignments or annotations.

Track Types#

Current track types include:

Track Type	Description	Associated File Formats
annotation	Non-quantitative genome annotations such as genes. This is the most generic track type.	bed, gff, gff3, gtf, bedpe, and others
wig	Quantitative genomic data, such as ChIP peaks and alignment coverage.	wig, bigWig, bedGraph
alignment	Sequencing alignments.	bam, cram
variant	Genomic variants	vcf
seg	Segmented copy number data.	seg
mut	Mutation data, primarily from cancer studies.	maf, mut
interact	Arcs representing associations or interactions between 2 genomic loci.	bedpe, interact, bigInteract
gwas	Genome wide association data (manhattan plots)	gwas, bed
arc	RNA secondary structure	bp, bed
junction	RNA splice junctions	bed
qtl	Quantitative trait locus	qtl
pytor	Copy number analysis	pytor, vcf
merged	Overlayed wig tracks

Configuring Tracks#

Tracks can be added during initial browser configuration, or via the browser API with the loadTrack function. In both cases a track is configured with an options object. For example, the following object creates a gene annotation track from an indexed BED file. The track will open initially in "expanded" mode.

{
      name: "Genes",
      type: "annotation",
      format: "bed",
      url: "<url to your bed file>",
      displayMode: "EXPANDED"
    }

Configuration Options for all track types#

Property	Description	Default
type	Track type	No default. If not specified, type is inferred from file format
sourceType	Type of data source. Valid values are "file", "htsget", and "custom"	file
format	File format	No default. If not specified format is inferred from file name extension
name	Display name (label). Required
url	URL to the track data resource, such as a file or webservice, or a data URI. As of release 2.5.2 the url property can be a function or promise that returns or resolves to a url string.
indexURL	URL to a file index, such as a BAM .bai, tabix .tbi, or tribble .idx file. Notes: For indexed file access the index URL is required, if absent the entire file will be read. As of release 2.5.2 the indexURL property can be a function or promise that resolves to a URL string.
indexed	Flag provided to explicitly indicate the resource is not indexed. If a resource is indexed the indexURL should be provided in which case this flag is redundant. This flag can be used to load small BAM files without an index by setting to false
order	Integer value specifying relative order of track position on the screen. To pin a track to the bottom use Number.MAX_VALUE. If no order is specified, tracks appear in order of their addition.
color	CSS color value for track features, e.g. "#ff0000" or "rgb(100,0,100)".
height	Initial height of track viewport in pixels	50
minHeight	Minimum height of track in pixels	50
maxHeight	Maximum height of track in pixels	500
visibilityWindow	Maximum window size in base pairs for which indexed annotations or variants are displayed	1 MB for variants, 30 KB for alignments, whole chromosome for other track types
removable	If true a "remove" item is included in the track menu.	true
headers	http headers to include with each request. For example {"Authorization": "Bearer cn389ncoiwuencr"}.
oauthToken	OAuth token, or function returning an OAuth token. The value will be included as a Bearer token with each request. See Oauth Support