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IGV User Guide
User Interface
Main Window
Menu Bar
Tool Bar
Pop-up Menus
Preferences
Color Legends
Keyboard Shortcuts
Starting IGV
Navigating
Loading a Genome
Viewing the Reference Genome
Sequence Track Options
Feature Track Options
Loading Data and Attributes
Viewing Data
Default Display
Changing the Display
Expression Data
RNAi Data
Segmented Data
GWAS Data
Viewing Alignments
Interpreting Color by Insert Size
Interpreting Color by Pair Orientation
Splice Junctions
Viewing Variants
Mutation Files
VCF Files
Gene List 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
External Control of IGV
Controlling IGV through a Port
Running IGV with a batch file
Creating HTML Links to IGV
igvtools
Running igvtools from the Command Line
Running igvtools from the IGV Interface
IGV 2.0 Feature Guide
New File Formats
New Toolbar Features
New Sequence Track Pop-up Menu Options
New NGS Functionality
File Formats
File Extension Identifies Format
Recommended File Formats
BAM
BED
BedGraph
bigBed
bigWig
Birdsuite Files
CBS
CN
Cufflinks Files
Custom File Formats
Cytoband
FASTA
GCT
genePred
GFF
GISTIC
Goby
GWAS
IGV
LOH
MAF (Multiple Alignment Format)
MAF (Mutation Annotation Format)
Merged BAM File
MUT
PSL
RES
SAM
Sample Information
chrom.sizes
SEG
SNP
TAB
TDF
Track Line
Type Line
VCF
WIG
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.x
IGV 2.1.x
IGV 2.2.x
IGV 2.3.x
Credits
Contact
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IGV User Guide
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Viewing Variants
Mutation Files
VCF Files
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