Custom File Formats

IGV 2.0 supports custom specification of columns for the ".igv" file format. To use this, include a column specifier directive at the head of the file. The column directive line starts with #column, followed by one or more column specifiers of the form key=value. Valid keys are listed in the following table.

Key Value
chr index of the chromosome column (required)
start index of the start position column (required)
end index of the end position column (optional)
probe index of a probe or description column (optional)
data either a single index, or a range in the form of 5-10, of the data columns (required)

Note: If a single value is entered for the data column, it is interpreted as the "first" data column. All columns starting with this value are assumed to contain data. To specify exactly one column, use a range (e.g., 5-5) to specify the 5th column.

Example:

 

#columns chr=7 start=8 probe=2 data=4-5 #coords=1 Index TargetID ProbeID_A sample 1 methylation sample 2 methylation GENOME_BUILD CHROMOSOME POSITION 60 cg00002593 25796427 0.7642099 0.7426524 37 1 1258656 21 cg00000957 65648367 0.8172337 0.8323303 37 1 5859840 ....