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  • IGV User Guide
    • User Interface
      • Main Window
      • Menu Bar
      • Tool Bar
      • Pop-up Menus
      • Preferences
      • Color Legends
      • Keyboard Shortcuts
    • Navigating the View
    • Loading a Genome
    • External Control of IGV
      • Controlling IGV through a Port
      • Running IGV with a batch file
      • Creating HTML Links to IGV
    • Viewing the Reference Genome
      • Sequence Track Options
      • Feature Track Options
    • Loading Data and Attributes
    • Viewing Data
      • Default Display
      • Changing the Display
      • Segmented Data
      • GWAS Data
      • RNA Secondary Structure
    • Viewing Alignments
      • Interpreting Color by Insert Size
      • Interpreting Color by Pair Orientation
      • Interpreting Color by Bisulfite Mode
      • Splice Junctions
      • Sashimi Plot
    • Viewing Variants
      • MAF Mutation Files
      • VCF Variant Files
    • Multi-Locus View
    • Regions of Interest
    • Sample Attributes
    • Sorting, Grouping, and Filtering
    • Saving and Restoring Sessions
    • Server Configuration
      • Configuring a Genome Server
      • Configuring a Data Server
      • Password Protected Directories
    • igvtools
      • Running igvtools from the Command Line
      • Running igvtools from the IGV Interface
    • Motif Finder
    • BLAT search
  • File Formats
    • BAM
    • BED
    • BedGraph
    • BEDPE
    • bigBed
    • bigWig
    • Birdsuite Files
    • broadPeak
    • CBS
    • Chemical Reactivity Probing Profiles
    • chrom.sizes
    • CN
    • Custom File Formats
    • Cytoband
    • FASTA
    • GCT
    • CRAM
    • genePred
    • GFF/GTF
    • GISTIC
    • Goby
    • GWAS
    • IGV
    • LOH
    • MAF (Multiple Alignment Format)
    • MAF (Mutation Annotation Format)
    • Merged BAM File
    • narrowPeak
    • PSL
    • RES
    • RNA Secondary Structure Formats
    • SAM
    • Sample Info (Attributes) file
    • SEG
    • TDF
    • Track Line
    • Type Line
    • VCF
    • WIG
  • Tutorial Videos
  • Hosted Genomes
  • FAQ
  • Release Notes
    • IGV 1.1
    • IGV 1.2
    • IGV 1.3
    • IGV 1.3.1
    • IGV 1.4
    • IGV 1.5.x
    • IGV 2.0 Feature Guide
      • New File Formats
      • New Toolbar Features
      • New Sequence Track Pop-up Menu Options
      • New NGS Functionality
    • IGV 2.0.x
    • IGV 2.1.x
    • IGV 2.2.x
    • IGV 2.3.x
    • IGV 2.4.x
    • IGV 2.5.x
    • IGV 2.6.x
    • IGV 2.7.x
    • IGV 2.8.x
    • IGV 2.9.x
    • IGV 2.10.x
    • IGV 2.11.x
    • IGV 2.12.x
    • IGV 2.13.x
    • IGV 2.14.x
    • IGV 2.15.x
    • IGV 2.16.x
  • Credits

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Broad Institute
and the Regents of the
University of California

 

Home › IGV User Guide › Viewing Data

Viewing Data

  • Default Display
  • Changing the Display
  • Segmented Data
  • GWAS Data
  • RNA Secondary Structure
‹ Loading Data and Attributes up Default Display ›