Batch scripts

Batch scripts are used to automatically execute a series of IGV commands.

How to run a batch script#

Select Tools > Run Batch Script to load a text file that contains a series of commands for IGV to execute.

Example script#

The following example script loads a BAM file and takes a series of snapshots at different loci. The snapshot images are saved in the specified directory.

genome hg18  
snapshotDirectory mySnapshotDirectory 
load myfile.bam 
goto chr1:65,289,335-65,309,335  
sort position  
goto chr1:113,144,120-113,164,120  
sort base  
goto chr4:68,457,006-68,467,006  
sort strand  

Script commands#

The batch script file is a plain text file with one command per line. Arguments are delimited by spaces (NOT tabs). Lines beginning with # or // are skipped. See the table below for a complete list of supported 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. See below for a list of valid options.
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.
goto locus or listOfLoci
group option tagNameOrPosition Alignment tracks only. Group alignments by the specified option. See below for a list of 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.
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 "" 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.
scrollToTop Scroll all panels to the top of the view. This is useful after loading a large number of tracks, which tracks loaded first scrolled out of view.
separate overlaidTrackName Separate an overlaid track into its constituitive tracks. This undos overlay.
setAltColor colorString trackName Set the track "altColor", used for negative values in a wig track or negative strand features. See description of setColor below.
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.
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 element delimited list for min,max. As of IGV 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.
clearAccessTokens Clears all access tokens.

ColorBy option values#

Group option values#

Sort option values#

Segmented copy number#