Tracks

Track Types

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. Current track types include:

Track Type	Description	Associated File Types
annotation	For displaying non-quantitative genome annotations such as genes. This is the most generic track type.	BED, GFF
wig	For displaying quantitative genomic data, such as ChIP peaks and alignment coverage.	WIG, bigWig, bedGraph
alignment	For displaying read alignments.	BAM
variant	For displaying genome variants.	VCF
seg	For displaying segmented copy number data.	SEG

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 a JSON-like 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",
      sourceType: "file",
      url: "//igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.collapsed.bed",
      indexURL: "//igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.collapsed.bed.idx",
      displayMode: "EXPANDED"
    }

####1) 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", "gcs" for Google Cloud Storage, and "ga4gh" for the Global Alliance API	"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. Required
indexURL	URL to a file index, such as a BAM .bai, Tabix .tbi, or Tribble .idx file.
indexed	Flag used to indicate if a file is indexed or not. If indexURL is provided this flag is redundant, its main purpose is to indicate that a file is not indexed.
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
autoHeight	If true, then track height is adjusted dynamically, within the bounds set by minHeight and maxHeight, to accomdodate features in view	true
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

####2) Options for tracks of type = "annotation"####

Property	Description	Default
displayMode	Annotation display mode, one of "COLLAPSED", "EXPANDED", "SQUISHED"	"COLLAPSED"
expandedRowHeight	Height of each row of features in "EXPANDED" mode	30
squishedRowHeight	Height of each row of features in "SQUISHED" mode	15
nameField	For GFF/GTF file formats. Name of column 9 property to be used for feature label	"Name"
maxRows	Maximum number of rows of features to display	500
searchable	If true, feature names for this track can be searched for. Use this option with caution, it is memory intensive. This option should will not work with indexed tracks.	false

####3) Options for tracks of type = "wig"####

Property	Description	Default
min	Sets the minimum value for the data (y-axis) scale. Usually zero.	0
max	Sets the maximum value for the data (y-axis) scale.	No default. If value is missing or set to undefined, the track will autoscale
color	Track color.	"rgb(150,150,150)"

####4) Options for tracks of type = "alignment"####

Property	Description	Default
viewAsPairs	If true, paired reads are drawn as a single alignment.	false
pairsSupported	If false, mate information in paired reads is ignored during downsampling and the 'View as Pairs' option is removed from the alignment track menu.	true
deletionColor	Color of line representing a deletion	"black";
skippedColor	Color of line representing a skipped region (e.g. splice junction)	"rgb(150, 170, 170)";
insertionColor	Color of marker for insertions	"rgb(138, 94, 161)";
negStrandColor	Color of alignment on negative strand. Applicable if colorBy = "strand"	"rgba(150, 150, 230, 0.75)";
posStrandColor	Color of alignment or position strand. Applicable if colorBy = "strand"	"rgba(230, 150, 150, 0.75)";
colorBy	Alignment color option: one of "none", "strand", "firstInPairStrand", or "tag". Specify tag with colorByTag	"none"
colorByTag	Specific tag to color alignment by.
bamColorTag	Specifies a special tag that explicitly encodes an r,g,b color value. Default value is "YC". If "YC" does not encode an r,g,b color value set bamColorTag to null. Must also set "colorBy" to "tag" to enable this option.	"YC"
samplingWindowSize	Window (bucket) size for alignment downsampling in base pairs	100
samplingDepth	Number of alignments to keep per bucket. WARNING: Setting this sampling depth to a high value will likely freeze the browser when viewing areas of deep coverage.	50.
maxRows	Maximum number of rows of alignments to display. Note: due to a limit on canvas height the maximum value for this parameter is ~2300 at the default row height of 14.	1000
alignmentRowHeight	Height in pixels of an alignment row when in expanded mode	14
filter	Alignment filter object. See table 4b

####4a) Options for GA4GH alignment tracks (sourceType = "ga4gh")####

Property	Description	Default
url	URL to the ga4gh endpoint (e.g. https://www.googleapis.com/genomics/v1beta2). Required
readGroupSetIds	ID of the read group set represented by this track. (e.g. 'CMvnhpKTFhCjz9_25e_lCw'). Required

####4b) Alignment filter object

Property	Description	Default
vendorFailed	filter alignments marked as failing vendor quality checks (bit 0x200)	true
duplicates	filter alignments marked as a duplicate (bit 0x400)	true
secondary	filter alignments marked secondary (bit 0x100)	false
supplementary	filter alignments marked as supplmentary (bit 0x800)	false
mqThreshold	filter alignments with mapping quality < supplied value (a number)	0

####5) Options for tracks of type = "variant"####

Property	Description	Default
displayMode	Display option. COLLAPSED => show variants only, SQUISHED and EXPANDED => show calls.	EXPANDED
homvarColor	CSS color used to represent homozygous non-reference calls.	"rgb(17,248,254)"
hetvarColor	CSS color used to represent heterozygous calls.	"rgb(34,12,253)"
homrefColor	CSS color used to represent homozygous reference calls.	"rgb(200, 200, 200)"

####5a) Options for GA4GH variant tracks (sourceType = "ga4gh")####

Property	Description	Default
url	URL to the ga4gh endpoint (e.g. https://www.googleapis.com/genomics/v1beta2). Required
variantSetId	ID of the variant set represented by this track. (e.g. '10473108253681171589'). Required
callSetIds	Array of GACallSet IDs to include with track. Optional. If omitted, all call sets are included