Recommended File Formats

Recommended File Formats

The following table lists recommended file formats for data types. Tip: Using igvtools to convert a source data file to a binary TDF file can reduce loading time and improve performance.

Source Data Recommended File Formats
ChIP-Seq, RNA-Seq

TDF format. Use the igvtools package (count command) to generate a binary read count density file in TDF format. Load the resulting TDF file into IGV.

Copy number

CN format, SNP format

Log values: If copy number data contains negative values, IGV assumes they are scaled log values and displays them without modification. If copy number data contains all positive values, IGV assumes they are unscaled. It centers the unscaled values around 2 (1 for allele specific files), log transforms them (logValue = log2(copyNumber / 2)), and displays the log values.

Gene expression data GCT format, RES format
Genome annotations GFF or GFF3 format, BED format
GISTIC data GISTIC format
LOH data LOH format
Mutation data MUT format
RNAi data GCT format (filename must end with this extension: .rnai.gct)
Segmented data SEG format, CBS format
Sequence alignment data SAM format (must be sorted), BAM format (must be indexed)
Any numeric data IGV format, TAB format, WIG format