Integrative Genomics Viewer, popularly known as IGV, is one of the popular tools to visualize High-throughput sequencing data alignment and genome alteration (SNV, InDel) in an interactive mode. This tutorial gives a basic understanding of IGV interface and NGS data browsing.

1. Integrative Genomics Viewer (IGV)
Samarth Kulshrestha, Data Analyst
National Institute of Biomedical Genomics, Kalyani
India

2. ● Overview
– Why IGV
– IGV Availability
● Machine requirements
● IGV interface
● IGV features (NGS Data)
– Searching Pattern, Viewing Alignment
● Variant visualization
Outline

3. ● IGV is a visualization tool of large data types
including BAM, BED, VCF, GFF etc.
● View large datasets easily (DNAseq, RNAseq, Microarray).
● Faster navigation or browsing.
● Can run locally on machine.
● User friendly interface.
● Freely available for academic use.
Why IGV?

4. ● IGV is a visualization tool of large data types
including BAM, BED, VCF, GFF etc.
● View large datasets easily (DNAseq, RNAseq, Microarray).
● Faster navigation or browsing.
● Can run locally on machine.
● User friendly interface.
● Freely available for academic use.
Why IGV?

5. https://www.broadinstitute.org/igv/
Availability

6. IGV Binary distribution
1) Download and extract the binary distribution
archive in a folder.
2) To launch IGV using command line in
Linux/Mac, follow instructions in the “readme” file.
3) To launch IGV using Windows operating
system, use “igv.bat”

7. 1) Operating System:
Windows, Linux, Macintosh
2) Java 6 or later.
Machine requirement
NOTE: Newer IGV version requires Java 7 or later

8. To start IGV from the command line (linux):
A) Type igv.sh in terminal and press ENTER key- igv.sh
Track Window
Search window Refresh button Zoom in/out
Chromosome
ideogram
RefSeq
genes
IGV Interface

9. 1) Switching Genome assembly.
2) File formats
3) Data Browsing
4) Loading BAM files.
5) Searching patterns:
A) Chromosome based.
B) Gene based.
C) Coordinates based.
6) Viewing Alignments
7) Viewing Variants
A) Transition
B) Transversion
C) Insertion
D) Deletion
IGV features

10. Available Genome assemblies
Including Human hg19, Human hg18 etc.
1) Switching genomes

11. 2) File formats
File Format Data Type
CBS, CN, SEG Copy Number
LOH LOH
GISTIC GISTIC data
RES Gene expression
BAM, SAM Sequence alignment
GWAS Genome-wide association
study data

12. A) Gene based:A) Gene based: TP53TP53
B) Coordinate based:B) Coordinate based: chr17:7578115-7578115chr17:7578115-7578115
C) Show all bases optionC) Show all bases option
D) Export alignment and save it.D) Export alignment and save it.
3) Data browsing
Zoom in and Zoom out
Search window
Chromosome drop-down
Frequently used
buttons
Pop-up information window

13. Click hereClick here 4) Loading BAM files
cont..

14. Click hereClick here
Select yourSelect your
BAM filesBAM files
cont..

15. Loaded Normal
BAM file
Loaded Tumor
BAM file
Coverage track
Coverage track
RefSeq genes

16. 1)1) Chromosome basedChromosome based
2)2) Gene based: Look for TP53Gene based: Look for TP53
3) Coordinate based: chr17:7577482-75775463) Coordinate based: chr17:7577482-7577546
5) Searching Patterns

17. Select desiredSelect desired
chromosome from thischromosome from this
drop down menu bardrop down menu bar
Sequence readsSequence reads
A) Chromosome based

18. Gene based
search
B) Gene Based

19. Gene based
search
Coordinate
based search
C) Coordinate based

20. Type ATM in search windowType ATM in search window
A)
6) Viewing Alignment
cont..

21. Type ATM in search windowType ATM in search window
A)
B)
150 Kb
cont..

22. Type ATM in search windowType ATM in search window
A)
B)
C)

23. Alignment windowAlignment window
Exons Intron
NOTE: Use arrow keys OR scroll bar to scroll down Alignment window
Coverage Track
Click and drag- left/Right
cont..

24. Show all bases
Alanine: Green
Guanine: Orange
Thymine: Red
Cytocine: Blue
cont..

25. Export Alignments: This option will extract all the reads in the searched window in
.sam format
cont..

26. Reads color based on
insert size

27. Transition
cont..
7) Viewing Variants

28. Transition Transversion
BAM
Files
cont..

29. Insertion
cont..
Insertion

30. DeletionInsertion
BAM
Files
1 base
deletion

31. Thank You