Downloading igvtools

The igvtools utilities can be downloaded from the Downloads page on the IGV website. 

Starting with shell scripts

The igvtools utilities can be invoked, with or without the graphical user interface (GUI), from one of the following scripts:

     igvtools (command-line version for Linux and  MacOS 10.x)
     igvtools_gui (GUI version for Linux and  MacOS 10.x)
     igvtools_gui.command (alternate double-clickable GUI version for MacOS 10.x)

     igvtools.bat (command-line version for Windows)
     igvtools_gui.bat (GUI version for Windows)

Once the GUI version has been launched, the commands and options are the same as when you run igvtools from the IGV interface.

The general form of the command-line version is:

     igvtools [command] [options][arguments]     --or--     igvtools.bat [command] [options][arguments]

Recognized commands, options, arguments, and file types are described below.

Starting with Java

igvtools can also be started directly using Java.  This option allows more control over Java parameters, such as the maximum memory to allocate.  In the example shown below, igvtools is started with 1500 MB of memory allocated and launched in the location where you have unpacked IGVTools.

      java -Xmx1500m --module-path=lib @igv.args --module=org.igv/org.broad.igv.tools.IgvTools [command] [options][arguments]

To start with a GUI the command is 

     java -Xmx1500m --module-path=lib @igv.args --module=org.igv/org.broad.igv.tools.IgvTools gui

Note that the command line has become more complex with Java 11 compared to Java 8.  We recommend the shell scripts above for most users.

Memory settings

The igvtools scripts allocate a fixed amount of memory.  If this is more than the amoount available on your platform, you will get an error along the lines of "Could not start the Virtual Machine".  If this happens you will need to edit the scripts to reduce the amount of memory requested, or use the Java startup option.  The memory is set via a "-Xmx" parameter. For example  -Xmx1500m requests 1500 MB,  -Xmx1g requests 1 gigabyte.

For more information about other settings, see the downloaded file igvtools_readme.txt.

Commands

toTDF

The toTDF command converts a sorted data input file to a binary tiled data (.tdf) file. Use this command to pre-process large datasets for improved IGV performance. 

Supported input file formats are: .wig, .cn, .snp, .igv, and .gct.

Note: This tool was previously known as tile

Usage:

          igvtools toTDF [options]  [inputFile] [outputFile] [genome]

Required arguments:

          inputFile    The input file (see supported formats above).

          outputFile   Binary output file.  Must end in ".tdf".

          genome      A genome id or path to a .chrom.sizes or .genome file.  Default is hg18.

Options:

 -z num  

Specifies the maximum zoom level to precompute. The default value is 7 and is sufficient for most files. To reduce file size at the expense of IGV performance this value can be reduced.

  -f  list    

A comma delimited list specifying window functions to use when reducing the data to precomputed tiles.   Possible values are min, max, and mean.  By default only the mean is calculated.

-p file   

Specifies a .bed file to be used to map probe identifiers to locations.  This option is useful when preprocessing . gct files.  The .bed file should contain 4 columns:
                          chr start end name
where name is the probe name in the .gct file.

Example:

          igvtools toTDF -z 5  copyNumberFile.cn copyNumberFile.tdf hg18

Notes:

Data file formats, with the exception of .gct files, must be sorted by start position.  Files can be sorted with the sort command described below.  Attempting to preprocess an unsorted file will result in an error.

Count

The count command computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in ChIP-seq experiments. By default, the resulting file will be displayed as a bar chart when loaded into IGV.

Supported input file formats are: .sam, .bam, .aligned, .psl, .pslx, and .bed.

Usage:

          igvtools count [options] [inputFile] [outputFile] [genome]

Required arguments:

          inputFile    The input file (see supported formats above).

         outputFile   The output file, which can be binary .tdf or ASCII .wig format.

The output filename must end in ".tdf" or ".wig", or be the special string "stdout". To indicate that you want to output both a .tdf and a .wig file, list both output filenames as a single string, separated by a comma with no other delimiters. If the output file is named "stdout" the output will be written to the standard output stream in .wig format.

          genome      A genome id or path to a .chrom.sizes or .genome file.  Default is hg18.

Options:

-z, --maxZoom num

Specifies the maximum zoom level to precompute.

-w, --windowSize num

The window size over which coverage is averaged. Defaults to 25 bp.

 -e, --extFactor num

The read or feature is extended by the specified distance in bp prior to counting. This option is useful for chip-seq and rna-seq applications. The value is generally set to the average fragment length of the library minus the average read length.

--preExtFactor num

The read is extended upstream from the 5' end by the specified distance.

--postExtFactor num

Effectively overrides the read length, defines the downstream extent from the 5' end. Intended for use with preExtFactor.

-f, --windowFunctions list

A comma delimited list specifying window functions to use when reducing the data to precomputed tiles. Possible values are min, max, mean, median, p2, p10, p90, and p98. The "p" values represent percentile, so p2=2nd percentile, etc.

--strands [arg]

By default, counting is combined among both strands. This setting outputs the count for each strand separately. Legal argument values are 'read' or 'first'. 'read' Separates count by 'read' strand, 'first' uses the first in pair strand".  Results are saved in a separate column for .wig output, and a separate track for TDF output.

--bases

Count the occurrence of each base (A,G,C,T,N). Takes no arguments. Results are saved in a separate column for .wig output, and a separate track for TDF output.

--query [querystring]

Only count a specific region. Query string has syntax <chr>:<start>-<end>. e.g. chr1:100-1000. Input file must be indexed. 

--minMapQuality [mqual]

Set the minimum mapping quality of reads to include. Default is 0.

--includeDuplicates

Include duplicate alignments in count. Default false. If this flag is included, duplicates are counted. Takes no arguments

--pairs

Compute coverage from paired alignments counting the entire insert as covered. When using this option only reads marked "proper pairs" are used.

Example:

          igvtools count -z 5 -w 25 -e 250 alignments.bam  alignments.cov.tdf  hg18

Notes: 

The input file must be sorted by start position. See the sort command below.

Index

Creates an index for an alignment or feature file. Index files are required for loading alignment files into IGV, and can significantly improve performance for large feature files. Note that the index file is not directly loaded into IGV. Rather, IGV looks for the index file when the alignment or feature file is loaded. This command does not take an output file argument. Instead, the filename is generated by appending ".sai" (for alignments) or ".idx" (for features) to the input filename as IGV relies on this naming convention to find the index . The input file must be sorted by start position (see sort command, below). 

Supported input file formats are: .sam, .bam, .aligned, .vcf, .psl, and .bed.

Usage:

          igvtools index [inputFile]

Notes:

The "sai" index is an IGV format, it does not work with samtools or any other application.

Sort

Sorts the input file by start position, as required.

Supported input file formats are: .cn, .igv, .sam, .bam, .aligned, .psl, .bed, and .vcf.

Usage:

          igvtools  sort [options] [inputFile]  [outputFile]

Required arguments:

          inputFile 

          outputFile 

The special string "stdout" can be used as [outputFile], in which case the output will be written to the standard output stream instead of a file.

Options:

  -t tmpdir 

Specify a temporary working directory.  For large input files this directory will be used to store intermediate results of the sort. The default is the users temp directory.

  -m maxRecords 

The maximum number of records to keep in memory during the sort. The default value is 500000. Increase this number if you receive "too many open files" errors. Decrease it if you experience "out of memory" errors.

Version

  Prints the igvtools version number to the console.