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Usage

Command line usage

General way to execute VDJtools routines would be the following,

java -Xmx16G -jar vdjtools.jar RoutineName [arguments] -m metadata.txt output/prefix

Output prefix could be either an output directory name (if ended with /) or an output file prefix. Most VDJtools routines will append the prefix with an intuitive suffix and extension.

The -m metadata.txt argument specifies a metadata file with relative sample paths, sample names and any other information to provide this information later in analysis. For more details, see the :ref:`metadata` section.

Alternatively, -m argument could be substituted with a space-separated list of files, e.g.

java -Xmx16G -jar vdjtools.jar RoutineName sample1.txt[.gz] sample2.txt[.gz] ... output/prefix

Whether not explicitly used (such as in "...Plot" routines) and applicable, plotting is turned on with -p argument.

The -h argument will bring up help message for specified routine.

Warning

Consider allocating sufficient memory for Java Virtual Machine when running the pipeline. To do so, execute the java with the -Xmx argument, e.g.:

java -Xmx16G -jar vdjtools.jar RoutineName [arguments]

If insufficient amount memory is allocated, the Java Virtual Machine could drop with a Java Heap Space Out of Memory error.

Warning

Due to JAR loading overhead, running VDJtools for a batch of samples should be preferred to running VDJtools separately for each sample if possible. See :ref:`metadata` section for more details.

Tip

Some routines could be memory demanding, especially when running sample intersection/joining/pooling with a high number of large (~1,000,000 clonotypes) datasets. Setting the -Xmx argument to 20-60Gb of memory should be enough for most purposes, e.g. 100 samples with 500,000 clonotypes on average.

Another way to work this around is to down-sample datasets to ~100,000 reads each using the :ref:`downsample` routine.

Importing clonotype tables

In order to proceed with VDJtools analysis datasets should be converted to VDJtools format (see :ref:`vdjtools_format`). To do this run either of the following commands:

java -Xmx16G -jar vdjtools.jar Convert -S software -m metadata.txt ... output_dir/

or

java -Xmx16G -jar vdjtools.jar Convert -S software sample1.txt[.gz] sample2.txt[.gz] ... output_dir/

An additional -c flag could be set to compress output files.

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