# This section contains CASAVA parameters for PROJECT_CONFIGURATION

[PROJECT_CONFIGURATION]
QVCutoff                        90
QVCutoffSingle                  10
alignabilityBatchSize           15000000
alignabilityForceRegenerate     0
alignabilityReadLength          30
alignabilitySuppressWarnings    0
appVersion                      CASAVA-1.8.2
applicationType                 RNA
bamWholeGenome                  0
barcodes                        
binSizeBuild                    50000000
binSizeProject                  50000000
buildId                         97cb002d196be496cc2e6f67ef8a2a49
chromNameSource                 contigName
chromNameValidation             on
chromosomes                     chr22
cmdGunzip                       gunzip
cmdGzip                         gzip
cmdSamtools                     /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/samtools
configured                      1
consensusIncludeIndels          0
currentRunId                    22_54_32_18_10_11
dataSetSuffix                   
dirBuild                        /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008
dirBuildExport                  /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/export
dirBuildParsed                  /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Parsed
dirBuildTemp                    /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/tmp
dirRefSeq                       /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes
extraBltArgs                    
featureFileName                 
genesListPath                   
ignoreMissingMetadata           0
indelsAlignScoreThresh          100
indelsCovCutoff                 3
indelsErrorRate                 
indelsMinContext                6
indelsMinCoverage               1
indelsMinGroupSize              3
indelsPrasThreshold             6
indelsSaveTempFiles             1
indelsSdFlankWeight             5
indelsSpReadThresholdClusters   5
indelsSpReadThresholdIndels     25.0
indelsSrasThreshold             10
isDenseAlleleCalls              1
isWorkflow                      1
isWorkflowAuto                  0
isWorkflowMake                  1
isWorkflowSGE                   0
jobsLimit                       
knownBases_chr22                34851311
lanes                           
makeFlags                       
maskRefSeqFiles                 chr22.fa
nonoverlappingExonCoordsParams  --verbose=1
poissonAlnCutoff                24
postRunCmd                      touch /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Build.finished
previousRunId                   22_54_32_18_10_11
projectId                       22_54_32_18_10_11
qualityType                     Phred64
read                            
readMode                        single
readSampleRateEnd               1.0
readSampleRateInput             1.0
readSampleRateStart             1.0
readSampleRateStep              0.1
refFlatFile                     /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Annotation/Genes/refFlat.txt.gz
refSeqCacheDirName              cachedRefSeq
refSeqLocked                    yes
regExpMitochondria              ^cM.fa$|^chrM.fa$|^cMT.fa$|^chrMT.fa$|^M$|^MT$
removeTemps                     ON
rmDup                           YES
rnaCountMethod                  readBases
samtoolsRefFile                 /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/chr22.fa
seqGeneMd2RefFlatParams         
sgeQmakeFlags                   -cwd -v PATH
singleScoreForPE                NO
skipVariableMetadata            1
snpMaxRatio                     3
snpThreshold                    10 
snpThreshold2                   6
sortBufferSize                  1984
sortMaxBatchSize                128
spliceJunction                  splice_sites-auto.fa
svRank_DepthWindow              1000
svRank_alnCutoff                24
svRank_covCutoff                10
svRank_maxFragmentSize          10000000
svRank_maxSD                    100
svRank_minObservations          5
svRank_minSingleScore           10
svRank_numLongSD                3
svRank_numShortSD               5
task2MakeParams                 --finishedPrefix tmp/make/tasks_2011-10-18_22-47-12.txt/
timeStamp_chr22                 1300361479
toNMScore                       -1
totalBases_chr22                49691432
variantsIndelCovCutoff          3.0
variantsIndelTheta              0.0001
variantsMDFilterCount           2
variantsMDFilterFlank           20
variantsMaxIndelSizePEDefault   300
variantsMaxIndelSizeSEDefault   50
variantsMinQbasecall            0
variantsMinVexp                 0.25
variantsNoCovCutoff             1
variantsSiteErrorDepDefault     0.6
variantsSiteErrorDepNoMismatch  0.35
variantsSnpCovCutoff            3.0
variantsSnpTheta                0.001
variantsSummaryMinQindel        20
variantsSummaryMinQsnp          20
verbose                         0
workflowFile                    /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/tasks.22_57_35_18_10_11.txt

[RUN_22_54_32_18_10_11]
_runId                          22_54_32_18_10_11
appVersion                      CASAVA-1.8.2
argv                            --skipVariableMetadata --samtoolsRefFile /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/chr22.fa --refFlatFile /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Annotation/Genes/refFlat.txt.gz --applicationType RNA --variantsNoCovCutoff --indelsSaveTempFiles --inSampleDir Aligned/Project_Demo/Sample_AR008 --outDir Build/Project_Demo/Sample_AR008/ --postRunCmd touch /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Build.finished --make --workflowFile Build/Project_Demo/Sample_AR008/tasks_2011-10-18_22-47-12.txt --task2MakeParams=--finishedPrefix tmp/make/tasks_2011-10-18_22-47-12.txt/
currentStatus                   finished
endTime                         22_57_35_18_10_11
force                           0
startTime                       22_54_32_18_10_11
target                          all
targets                         continue


[PROJECT_BIN_SIZES]
chr22                           1



# This section contains CASAVA parameters for BUILD_BIN_SIZES

[BUILD_BIN_SIZES]
chr22                           1