CASAVA CASAVA-1.7.0 PE DNA-Seq Usage
Added by CASAVA, last edited by CASAVA on 03-11-10
Welcome
CASAVA CASAVA-1.7.0 PE DNA-Seq - CASAVA usage

NAME

    CASAVA (1.0)- Scripts necessary for creating CASAVA build

30 July 2008 - This is the Readme file written by Richard Carter, Lukasz Szajkowski.

SYNOPSIS

USAGE

PLUGIN 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_ #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 ${CASAVA_ --refSequences=${CASAVA_ #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 ${CASAVA_ --refSequences=${CASAVA_ #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_ --refSequences ${CASAVA_
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=TYPEtype 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 nameused 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 0minimum)
--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=NUMBERsets 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 -1off)
--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 cleanallows 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
TARGETS: bam cov2bin rnaRead poisson indels alignability
use
./run.pl --help for plugin target usage details
EXAMPLES:
EXAMPLES=/usr/local/casava-1.7.0/share/CASAVA-1.7.0/examples
EXAMPLES}/GERALD -l 4 \
EXAMPLES}/genomes/E_coli --snpCovCutoff=-1 --indelsCovCutoff=-1
EXAMPLES}/GERALD -l 4 \
EXAMPLES}/genomes/E_coli --snpCovCutoff=-1 --readMode=single
EXAMPLES}/RNA_UHR_GERALD -l 2 \
EXAMPLES}/genomes/human


 
Version 1.0 (18:15:09 03-11-10)
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