Usage

Quick Usage

RunIlluminaProcess.pl [options]

–config | -c S Path to configration file(required)

—svConfig | -sc S Path to structural variant configration file(optional)

–symLinkFlag | -sf I Flag for Keeping or removing the symolic links(1:Remove;2:Keep)(default:2)

—dataDirectory | -d S Path where all the files to be processed are located (required)

–outputDirectory | -o S Path where all the output files will be written (required)

Assuming you have setup the configuration file properly and you have SampleSheet.csv and title_file.txt in the dataDirectory you can run:

nohup perl RunIlluminaProcess.pl -c configuration.txt -sc configuration_sc.txt -d /path/to/fastq/files -o /path/to/output/directory

Detailed Usage

The behaviour of the prgram depends on the inputs in the configuration file:

In the configuration file the Process variable in section >Parameters tells pipeline following:

What does each number represent

Process Things Pipeline will do
1 Merge Fastq
2 Trimming, Mapping & sorting of SAM file giving you a BAM file
3 Mark Duplicates, Indel Realignment, Base Quality Recalibration
4 Metrics Calculation, QC Report Genaration and launching IMPACT-SV if given -sc flag specified
5 Variant Calling
6 Variant Filtering and Genotyping
7 Variant Annotation and Variant Filtering

Using different Process to run Pipeline

  1. To run the complete pipeline. Set the following in the configuration file:

    Process:1,2,3,4,5,6,7

  2. To run from Process 1. Set the following in the configuration file:

    ListOfFilesListOfFiles:
     fastq.list #where fastq.list contains all the fastq files to be proces, this needs to be an even number as it automatically pairs them.
    Process:2,3,4,5,6,7

  3. To run from the Process 3 to 7. Set the following in the configuration file:

    ListOfFiles:SortedBam.list (where SortedBam.list contains all the sorted bam files from Process 2 to be processed)
    Process:3,4,5,6,7

  4. To run from the Process 4 to 7. Set the following in the configuration file:

    ListOfFiles:RecalibratedBam.list (where Recalibrated.list contains all the recalibrated bam files from Process 3 to be processed)
    Process:4,5,6,7

Note:

For this to be sucessfull you should have the files from step 4 in the outputDirectory

  1. To run from the Process 5 to 7. Set the following in the configuration file:

    ListOfFiles:RecalibratedBam.list (where Recalibrated.list contains all the recalibrated bam files from Process 3 to be processed)
    Process:5,6,7

Note:

For this to be sucessfull you should have the files from step 5 in the outputDirectory

  1. To run from the Process 6 to 7. Set the following in the configuration file:

    ListOfFiles:RecalibratedBam.list (where Recalibrated.list contains all the recalibrated bam files from Process 3 to be processed)
    Process:6,7

Note:

For this to be sucessfull you should have the files from step 6 in the outputDirectory

  1. To run from the Process 7. Set the following in the configuration file:

    ListOfFiles:RecalibratedBam.list (where Recalibrated.list contains all the recalibrated bam files from Process 3 to be processed)
    Process:7

If you want to run each Process separetly that is also possible but you need to make sure that files from previous procss are present in the outputDirectory

Shell Script to run pipeline

There is also a helper shell script (Run_Pipeline_Example.sh) in the bin directory which will help to run the framework. Which looks like this:

Note:

Please comment out the lines using (#) according to the cluster type and analysis type.

##Run_Pipeline_Example.sh
#author:Ronak H Shah
#v1.0.1
##Path where the fastq are stored
export DATADIR=<Path for Data Directory>
##Path where the output shoud be written
export OUTDIR=<Path To Output Directory>
##Path to the IMPACT-Pipeline script
export PipelineScript=<Path to IMPACT-Pipeline Script>
##Path to Perl installation
export Perl=<Path to Perl>
##Project associated with the Run
export ProjectName=<ProjectName>
##Path to working directory where you will write the LSF/SGE outputs
export WorkingDir=<Path to write sge/lsf files>
##Path to configfile for running main IMPACT pipeline
export CONFIGFILE=<Path To Pipeline Configuration File>
##Path to structural variants pipeline configuration file
export SV_ConfigFile=<Path to SV detection configuration file>

##Run both IMPACT-Pipeline & SV Process on LSF
echo bsub -q sol -cwd ${WorkingDir} -J ${ProjectName} -e${ProjectName}.stderr -o ${ProjectName}.stdout -We 24:00 -R "rusage[mem=2]" -M 4 \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -sc {$SV_ConfigFile} -d ${DATADIR} -o ${OUTDIR}\"
bsub -q sol -cwd ${WorkingDir} -J ${PoolName} -e${ProjectName}.stderr -o ${ProjectName}.stdout -We 24:00 -R "rusage[mem=2]" -M 4 \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -sc {$SV_ConfigFile} -d ${DATADIR} -o ${OUTDIR}\"
##Run IMPACT-Pipeline on LSF
echo bsub -q sol -cwd ${WorkingDir} -J ${ProjectName} -e${ProjectName}.stderr -o ${ProjectName}.stdout -We 24:00 -R "rusage[mem=2]" -M 4 \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -d ${DATADIR} -o ${OUTDIR}\"
bsub -q sol -cwd ${WorkingDir} -J ${PoolName} -e${ProjectName}.stderr -o ${ProjectName}.stdout -We 24:00 -R "rusage[mem=2]" -M 4 \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -d ${DATADIR} -o ${OUTDIR}\"

##Run both IMPACT-Pipeline & SV Process on SGE
echo qsub -q test.q -wd ${WorkingDir} -N ${ProjectName} -l hvmem=2G,virtual_free=2G -pe smp 1 -b y \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -sc ${SV_ConfigFile} -d ${DATADIR} -o ${OUTDIR}\"
qsub -q test.q -wd ${WorkingDir} -N ${ProjectName} -l hvmem=2G,virtual_free=2G -pe smp 1 -b y \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -sc ${SV_ConfigFile} -d ${DATADIR} -o ${OUTDIR}\"
##Run both IMPACT-Pipeline on SGE
echo qsub -q test.q -wd ${WorkingDir} -N ${ProjectName} -l hvmem=2G,virtual_free=2G -pe smp 1 -b y \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -d ${DATADIR} -o ${OUTDIR}\"
qsub -q test.q -wd ${WorkingDir} -N ${ProjectName} -l hvmem=2G,virtual_free=2G -pe smp 1 -b y \"${Perl} ${PipelineScript} -c ${CONFIGFILE} -d ${DATADIR} -o ${OUTDIR}\"