Usage | : run.pl [options] |
-e, --exportDir=PATH | source directory PATH also known as GERALD directory or run directory |
-l, --lanes=NUMBER_LIST | list of the lanes to use |
-p, --projectDir=PATH | project directory PATH (where we keep CASAVA build) |
-r, --runId=STRING | unique identifier of each run |
-ref, --refSequences=PATH | PATH of the reference genome sequences |
OPTIONAL | (BEHAVIOUR) |
-a, --applicationType=TYPE | type of analysis [DNA, RNA] default DNA |
--postRunCmd=CMDLINE | executes CMDLINE after all tasks are finished |
-f, --force | ignore errors from previous run |
--help[=TARGET] | prints usage guide. If TARGET is specified, prints usage guide for the corresponding plugin target |
-rt, --removeTemps=ON/OFF | removes temporary data (default ON) |
--dirTemp | overrides default path for local temporary files |
--targets LIST | space-separated LIST of targets to run (default: all) |
-w, --workflow | instead of running the program generates the workflow definition file. |
-wa --workflowAuto | generates the workflow definition file and runs it. See --jobsLimit. |
-sa --sgeAuto | generates the workflow definition file and runs it on SGE (use with --sgeQueue) |
--jobsLimit | limit number of parallel jobs. Defaults: -1 (unlimited) for --sgeAuto. 1 for --workflowAuto. |
--sgeQueue | SGE queue name | used with --sgeAuto or --workflow (e.g: all.q) |
--workflowFile=FILE | overrides workflow file name. (default workflow..txt) |
--verbose=NUMBER | sets the console log verbose level (default 0 | minimum) |
--version | prints version information |
OPTIONAL | (ANALYSIS) |
--refFlatFile=PATH | PATH to UCSC refFlat.txt.gz file. The file must be gz-compressed. |
--seqGeneMdFile=PATH | PATH to NCBI seq_gene.md.gz file. The file must be gz-compressed. |
--snpThreshold=NUMBER | sets the |
SNPCaller primary allele threshold to NUMBER (default 10) |
--snpThreshold2=NUMBER | sets the |
SNPCaller secondary allele threshold to NUMBER (default 6) |
--snpMaxRatio=NUMBER | sets the |
SNPCaller max ratio to NUMBER (default 3) |
--snpCovCutoff=NUMBER | sets the |
SNPCaller coverage cutoff depth to NUMBER times the chromosomal mean. (default 3) |
Set this value to -1 to disable the coverage filter (recommended for RNA and targeted resequencing) |
-rm, --readMode | Runread-mode for all runs [paired, single] (default paired) |
--QVCutoff=NUMBER | sets the alleleCaller PE aligment score threshold to NUMBER (default 6) |
--QVCutoffSingle=NUMBER | sets the alleleCaller SE aligment score threshold to NUMBER (default 10) |
--singleScoreForPE=VALUE | sets the alleleCaller to filter reads with single score below QVCutoffSingle in PE mode YES|NO (default NO) |
--baseQualityCutOff=NUMBER | sets minimum base quality in allele caller (default 0) |
--qualityType=VALUE | Quality to probability scheme Phred64|Solexa64 (default Phred64) |
--toNMScore=NUMBER | minimum SE alignment score to put a read to NM (default -1 | off) |
--rmDup=YES|NO | Turn On/Off PCR duplicates removal in PE mode (default YES) |
--denseAlleleCalls | Leave empty rows out of the allele-call file (already set for RNA analysis) |
TARGETS | |
all | build targets that are pre-configured for the given analysis type. This is the default. |
export | loads the export files to export directory |
sort | sorts reads and moves them to bins in the build directory (Parsed_...), optionally also removes pcr duplicates |
allele | allele calling in the build directory |
snp | finds SNP and exports them to GFF format |
exp2sra | converts all export files from GERALD folders to a zipped fastq files and generates sra.xml |
clean | soft clean | allows to restart the build without removing project.conf and run.conf.xml |
allClean | removes all data |
snpClean | removes snp data |
sortClean | removes sort data |
alleleClean | removes allele data |
PLUGIN TARGETS | : bam cov2bin rnaRead poisson indels alignability |
use |
./run.pl --help for plugin target usage details |
EXAMPLES | : |
CASAVA_PATH=/usr/local/casava-1.7.0/bin
CASAVA_FEATURES=/usr/local/casava-1.7.0/share/CASAVA-1.7.0/examples/features
CASAVA_EXAMPLES | =/usr/local/casava-1.7.0/share/CASAVA-1.7.0/examples |
#Run default paired DNA analysis targets on test E_coli data run TestEColiPE lane 4
${CASAVA_PATH}/run.pl --runId=TestEColiPE --projectDir=./DNA_EColi_PE \
-e ${CASAVA_EXAMPLES | }/GERALD -l 4 \ |
--refSequences=${CASAVA_EXAMPLES | }/genomes/E_coli --snpCovCutoff=-1 --indelsCovCutoff=-1 |
#Run default single-ended DNA analysis targets on E_coli data run TestEColiSE lane 4
${CASAVA_PATH}/run.pl --runId=TestEColiSE --projectDir=./DNA_EColi_SE \
-e ${CASAVA_EXAMPLES | }/GERALD -l 4 \ |
--refSequences=${CASAVA_EXAMPLES | }/genomes/E_coli --snpCovCutoff=-1 --readMode=single |
#Run default RNA analysis targets on Human_UHR chromosome 22 data run TestRNAUHR lane 2
${CASAVA_PATH}/runRNA.pl --runId=TestRNAUHR --projectDir=./RNA_UHR \
--seqGeneMdFile=${CASAVA_FEATURES}/human/NCBI/Build36.3/seq_gene.md.gz \
-e ${CASAVA_EXAMPLES | }/RNA_UHR_GERALD -l 2 \ |
--refSequences ${CASAVA_EXAMPLES | }/genomes/human |