When you load genomic data, IGV displays the data in horizontal rows called tracks. Typically, each track represents one sample or experiment. For each track, IGV displays the track identifier, one or more attributes, and the data.
When loading a data file, IGV uses the file extension to determine the file format (see File Formats), the file format to determine the data type (Table 1), and the data type to determine the track default display options (Table 2).
| File Format |
Data Type |
Table 1. File Format Determines Data Type
| CBS, CN, MAF, SEG, SNP, VCF |
Copy number |
| LOH |
LOH |
| GCT |
Gene expression or RNAi |
| GISTIC |
GISTIC data |
| RES |
Gene expression |
| BAM, bam.list, Goby files, PSL, SAM |
Sequence alignments |
| BED, genePred, GFF, GFF3 |
Genome annotations |
| MUT |
Mutation |
| GWAS |
Genome-wide association study data |
| IGV, WIG, HDF5 file not created with alignment processor, bedgraph |
Other |
| Cytoband, FASTA |
Not applicable. Cytoband and sequence files for an imported genome. |
| Data Type |
Default Graph Type |
Default Data Range |
Default Colors |
Table 2. Data Type Determines Display Options
| Copy number |
Heatmap |
-1.5 to 1.5 |
Blue to red |
| Gene expression |
Heatmap |
-1.5 to 1.5 |
Blue to red |
| Chip |
Bar chart |
None, data is autoscaled |
Blue |
| DNA methylation |
Heatmap |
0 to 1
(methylation score) |
Green |
| Allele-specific copy number |
Heatmap |
-1.5 to 1.5 |
Blue to red |
| LOH |
Heatmap |
-1 to 1 |
Blue = LOH (1)
Yellow = Retained (0)
Red = Conflict (-1) |
| RNAi |
Heatmap |
-3 to 3 |
Red to blue |
| GWAS |
Scatter plot |
None, data is autoscaled |
Chromosome colors |
| Other |
Bar chart |
None, data is autoscaled |
Blue |
