igvteam/igv-mcp
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A Model Context Protocol (MCP) server for controlling IGV (Integrative Genomics Viewer) via socket commands.
Tools
Functions exposed to the LLM to take actions
new
Reset IGV to a clean state by unloading all data tracks
saveSession
Save the current IGV session
genome
Load a reference genome by ID or file path
load
Load data files (BAM, SAM, VCF, etc.)
goto
Navigate to a genomic locus
zoomin
Zoom in the view
zoomout
Zoom out the view
collapse
Collapse track to compact representation
squish
Squish track by reducing row height
expand
Expand track by increasing row height
setColor
Set the primary display color for tracks
renameTrack
Rename a track
region
Define a region of interest
group
Group alignment reads by properties
sort
Sort reads by various criteria
viewAsPairs
Toggle paired-end read visualization mode
setSequenceStrand
Set which DNA strand to display
setSequenceShowTranslation
Toggle translation display
overlay
Combine multiple wig tracks into a single overlaid track
separate
Separate an overlaid wig track into component tracks
snapshot
Capture a snapshot image of the current IGV view
snapshotDirectory
Set the directory where snapshots will be saved
maxPanelHeight
Set maximum height for track panels in snapshots
Prompts
Interactive templates invoked by user choice
No prompts
Resources
Contextual data attached and managed by the client