1. Integrative Genomics Viewer (IGV)
Satish C Bhalla, PhD
Department of Computer
Science and Engineering
Johnson C Smith University
Charlotte, NC

2. Integrative Genomics Viewer (IGV)
Visualization tool for exploring and analyzing large genome datasets
Work with prebuilt genomes or import a genome
View a variety of data such as expression data, NGS alignments, microarray, epigenomics, RNA-Seq, genomic annotations etc.
Run it locally on your desktop or launch it from the Broad Institute website.
Must register for launching or down loading.
IGV is a Java application
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3. Outline Launch or download IGV IGV user interface
Main Window
Tool Bar
Ex. 1- Load a genome and define a region of interest
Ex. 2 – Search for Bladder Cancer Gene - DAPK1
Ex. 3 - IGV Tools
Ex. 4 - SAMTOOLS
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4. Launch or Download IGV Launch from Broad Institute website:
Go to
The first time you sign on, you will need to register to download IGV.
Click on the first launch icon (Launch with 750MB); 750MB is the smallest memory available and is sufficient for most applications.
Download IGV
Alternatively, you may download IGV zip file and install on your desktop.
If you want to install and start IGV from command line (UNIX terminal) you will need the binary distribution.
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5. Launch or download IGV http://www. broadinstitute
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6. IGV Main Window (Source: IGV User Guide)
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7. Tool Bar
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8. Ex. 1- Load a genome and define a region of interest
Load a genome – Arabidopsis thaliana.
Select a chromosome – chr 1.
Define a region of interest.
Display the nucleotide sequence.
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9. Load a genome sequence Arabidopsis thaliana
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10. Select Chromosome 1
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11. Define region of interest Click and drag anywhere on the chromosome; zoom in
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12. Increase the zoom and display the nucleotide sequence
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13. Ex. 2 – Search for Bladder Cancer Gene - DAPK1
Load a prebuilt genome – Human hg19.
Search for a bladder cancer gene - DAPK1.
View the gene sequence.
Translate the nucleotide sequence to an amino acid sequence.
Copy sequence and save it to your hard drive.
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14. Load Human Genome - hg19 Click on chr 9
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15. Chromosome 9 Human Genome - hg19
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16. Search for a bladder cancer gene – DAPK1
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17. DAPK1 Gene Sequence
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18. Gene Sequence Translation
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19. Ex. 3 IGV Tools Use IGV Tools to sort a file, (use SORT command)
create an index file (use index command)
create a .tdf file, (use ‘to TDF’ command)
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20. IGV Tools: sort command Sort dnai1.reads.sam
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21. IGV Tools: index command create an index on dnai1. reads. sorted
IGV Tools: index command create an index on dnai1.reads.sorted.sam Output file: dnai1.reads.sorted.sam.sai
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22. IGV Tools: ‘toTDF’ command Convert dnai1. reads. sorted
IGV Tools: ‘toTDF’ command Convert dnai1.reads.sorted.sam to a binary tiled data file (.tdf)
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23. Ex. 4 SAMTOOLS Install SAMTOOLS
Make SAMTOOLS executable (use make command)
Use SAMTOOLS to:
Convert SAM file to a BAM file
Sort the BAM file (use sort command)
Create an index on BAM file (use index command)
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24. Install SAMTOOLS SAMTOOLS is an open source program.
Download latest version of samtools tar.bz2 (514.5 kB) from sourceforge or samtools website
Unzip and install.
Commands are given on the command line in the UNIX environment.
Basic usage: samtools <command> [options]
If you happen to be using Windows computer, you may buy a KNOPPIX (LINUX) DVD or download Linux on a cd and make it executable.
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25. How to make SAMTOOLS executable?
Start SAMTOOLS and make it executable with make command
Point to SAMTOOLS in the igvdata directory.
Right click > open in terminal
make
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26. Convert a SAM file to a BAM file with SAMTOOLS
./samtools view –b –S dnai1.reads.sam > dnai1_reads.bam
(Give the full path name of the input file such as: /media/sdb1/igvdata/ dnai1.reads.sam).
Note: You may convert SAM to BAM in Galaxy if you are familiar with it.
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27. Sort a BAM file
In order to create an index BAM file, it needs to be sorted first.
./samtools sort –m dnai1_reads.bam dnai1_reads_sorted.bam
Note: Modifier –m indicates the maximum amount of memory that can be used
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28. Create a BAM index file Create an index file on dnai1_reads.sorted.bam
./samtools index dnai1_reads_sorted.bam
dnai1_reads_sorted.sam.sai will be created and saved in the same directory as the input file.
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