Batch commands

Command	Parameters	Description
collapse	trackName	Collapses a given track. trackName is optional, if it is not supplied all tracks are collapsed.
colorBy	option tagName	Sets the "color by" option for alignment tracks. For option "TAG" also specify the tag name.
echo	param	Writes the value of "param" back to the response, or if param is not specified "echo".
exit		Exit (close) the IGV application.
expand	trackName	Expands a given trackName. trackName is optional, however, and if it is not supplied all tracks are expanded.
genome	genomeIdOrPath	Selects a genome by id, or loads a genome (or indexed fasta) from the supplied path. Note: this command will start a new session clearing any currently loaded tracks. It is recommended that the genome be specified as the first command in a script.
goto	locus or listOfLoci
group	option tagName	Alignment tracks only. Group alignments by the specified option. See below for valid option values. For option "TAG" also specify the tag name.
load	file	Loads a data or session file by specifying a full path to a local file or a URL. To explicitly specify a path to an index file use the optional "index=" parameter. For examples load foo.bam index=bar.bai
maxPanelHeight	height	Sets the number of vertical pixels (height) of each panel to include in image. Images created from a port command or batch script are not limited to the data visible on the screen. Stated another way, images can include the entire panel not just the portion visible in the scrollable screen area. The default value for this setting is 1000, increase it to see more data, decrease it to create smaller images. To capture the exact area visible on the screen set this value to -1.
new		Create a new session. Unloads all tracks except the default genome annotations.
overlay	overlaidTrackName trackNames	Overlay a list of tracks. trackNames is a space separated list. Spaces in track names must be replaced with %20. Release 2.12.0
preference	key value	Temporarily set the preference named key to the specified value. This preference only lasts until IGV is shut down. The complete set of preference keys are listed in the file "preferences.tab" here. The first column is the key, the third column is the value type. For select value types the permitted values follow as a list delimited by the character "|".
region	chr start end	Defines a region of interest bounded by the two loci (e.g., region chr1 100 200).
saveSession	filename	Save the current session. It is recommended that a full path be used for filename. IGV release 2.11.1
scrollToTrack	trackName	Scroll panel if neccessary so specified track is at the top
scrollToTop		Scroll all panels to top position. Useful prior to snapshots.
separate	overlaidTrackName	Separate an overlaid track into its constituitive tracks. This undos overlay. Release 2.12.0
setAltColor	colorString trackName	Set the track "altColor", used for negative values in a wig track or negative strand features. See description of setColor below. IGV release 2.11.1
setColor	colorString trackName	Set the track color. colorString can be a comma delimited rgb string with components in the range 0-255, for example 255,0,0, or a hex color string, for example FF0000. IGV release 2.11.1
setDataRange	rangeString trackName	Set the data range (scale) for all numeric tracks, or if a trackName is specified a specific track. rangeString is either a 2 comma delimited list for min,max. As of release 2.11.0 'auto' can be used for rangeString, which will set the track(s) to autoscale.
setLogScale	true/false trackName	Set the data scale to log (true) or linear (false). Optionally specify a track, if no track is specified all numeric tracks will be set.
setSequenceStrand	+ / -	Set the sequence strand to positive (+) or negative (-). Note this does not reverse the direction left-right.
setSequenceShowTranslation	true / false	Show or hide the 3-frame translation rows of the sequence track.
setSleepInterval	ms	Sets a delay (sleep) time in milliseconds. The sleep interval is invoked between successive commands.
setTrackHeight	height trackName	Set the specified track's height in integer units. trackName is required.
snapshotDirectory	path	Sets the directory in which to write images.
snapshot	filename	Saves a snapshot of the IGV window to an image file. If filename is omitted, writes a PNG file with a filename generated based on the locus. If filename is specified, the filename extension determines the image file format, which must be either .png or .svg.
sort	option locus direction	Sorts alignment or segmented copy number tracks. See below for valid option values. If supplied, the locus option can define a single position for alignments, or a range for copy number. If absent sorting will be based on the center position of the region in view for alignment tracks, or the average over the entire region in view for segmented copy number. If direction is specified and equal to reverse sort order is reversed. Locus must be specified if direction is specified.
squish	trackName	Squish a given trackName. trackName is optional, and if it is not supplied all annotation tracks are squished.
viewaspairs	trackName	Set the display mode for an alignment track to "View as pairs". trackName is optional.
setAccessToken	token host	Set an access token to be used in an ```Authorization: bearer" header for all requests to host. If host is omitted token is used for all requests. Since release 2.14.2
clearAccessTokens		Clears all access tokens. Since release 2.14.2

ColorBy option values

• BISULFITE
• FIRST_OF_PAIR_STRAND
• INSERT_SIZE
• LIBRARY
• LINK_STRAND
• MAPPED_SIZE
• MOVIE
• NOMESEQ
• NONE
• PAIR_ORIENTATION
• READ_GROUP
• READ_STRAND
• SAMPLE
• TAG
• UNEXPECTED_PAIR
• YC_TAG
• ZMW

Group option values

• ALIGNED_READ_LENGTH
• BASE_AT_POS
• FIRST_OF_PAIR_STRAND
• HAPLOTYPE
• LIBRARY
• MATE_CHROMOSOME
• MOVIE
• NONE
• PAIR_ORIENTATION
• PHASE
• READ_GROUP
• READ_ORDER
• REFERENCE_CONCORDANCE
• SAMPLE
• STRAND
• SUPPLEMENTARY
• TAG
• ZMW

Sort option values

Segmented copy number

• AMPLIFICATION
• DELETION

Alignments

• BASE
• FIRSTOFPAIRSTRAND
• INSERSTSIZE
• MATECHR
• POSITION
• QUALITY
• READGROUP
• READORDER
• READNAME
• SAMPLE
• STRAND
• ALIGNEDREADLENGTH