A comprehensive analysis framework for T-cell and B-cell repertoire sequencing data.

VDJtools is no longer maintained. See MiXCR for the software which succeeded VDJtools.

• vdjtools Main Site

• Module Name: vdjtools (see the modules page for more information)
• Singlethreaded
• environment variables set (where ${VER} matches the version loaded)
  • $VDJ_PATH=/usr/local/apps/vdjtools/${VER}
  • $VDJ_JAR=/usr/local/apps/vdjtools/${VER}/vdjtools-${VER}.jar
• Commands that utilize R must be run in a job with allocated local storage/lscratch.
• Commands using the circlize R library like PlotFancyVJUsage may fail with newer R/circlize versions. Unfortunately, this was not fixed before vdjtools stopped being supported.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load vdjtools

[user@cn3144 ~]$ java -Xmx4g -jar $VDJ_JAR
VDJtools V1.1.10

Run as $java -jar vdjtools-1.1.10.jar ROUTINE_NAME arguments

[Basic]
CalcBasicStats
CalcSpectratype
CalcSegmentUsage
PlotFancySpectratype
PlotSpectratypeV
PlotFancyVJUsage

[Diversity]
CalcDiversityStats
RarefactionPlot
PlotQuantileStats

[Overlap]
OverlapPair
CalcPairwiseDistances
ClusterSamples
TestClusters
TrackClonotypes

[Preprocessing]
ApplySampleAsFilter
FilterNonFunctional
FilterByFrequency
DownSample
Decontaminate
FilterBySegment
SelectTop

[Operation]
PoolSamples
JoinSamples
(Enrichment) -> Deprecated

[Annotation]
(ScanDatabase) -> moved to VDJdb since 1.0.5, please visit vdjdb.cdr3.net
CalcCdrAaStats
CalcDegreeStats
Annotate
SegmentsToFamilies

[Util]
FilterMetadata
SplitMetadata
Convert
RInstall

* Run with 'discard_scripts' option prior to ROUTINE_NAME to clean up R scripts upon execution

[user@cn3144 ~]$ java -Xmx4g -jar $VDJ_JAR CalcBasicStats -h
usage: CalcBasicStats [options] [sample1 sample2 sample3 ... if -m is not
                      specified] output_prefix
 -h                         display help message
 -m,--metadata    Metadata file. First and second columns should
                            contain file name and sample id. Header is
                            mandatory and will be used to assign column
                            names for metadata.
 -u,--unweighted            Will count each clonotype only once, apart
                            from conventional frequency-weighted
                            histogram.

[user@cn3144 ~]$ java -Xmx4g -jar $VDJ_JAR CalcBasicStats sample1 sample2 sample3

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. vdjtools.sh). For example:

#!/bin/bash
module load vdjtools
java -Xmx4g -jar $VDJ_JAR CalcBasicStats sample1 sample2 sample3

Submit this job using the Slurm sbatch command.

sbatch --mem=4g vdjtools.sh

Create a swarmfile (e.g. vdjtools.swarm). For example:

java -Xmx4g -jar $VDJ_JAR CalcBasicStats sample1 
java -Xmx4g -jar $VDJ_JAR CalcBasicStats sample2 
java -Xmx4g -jar $VDJ_JAR CalcBasicStats sample3

Submit this job using the swarm command.

swarm -f vdjtools.swarm -g 4 --module vdjtools