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Impact_BSUB_args
$BSUB -q $queue -J AD.$bamID.$$ -cwd $outdir -e AD.$bamID.$$.%J.stderr -o AD.$bamID.$$.%J.stdout -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$PERL $GenotypeAllele -fmv $cosmicHotspotVcf -bam $outdir/$bamFile -rf $Reference -s $SAMTOOLS -o $outdir -of $alleleDepthMutationOut -mof $mpileUpMutationOut -bi $bamID -mmq $MAPQ -mbq $BASQ -q $queue -b $BEDTOOLS -bsub $BSUB"";
$BSUB
-q
$BSUB -q $queue -J RSYNC.$stdBamId.$$ -cwd $outdir -e RSYNC.$stdBamId.$$.%J.stderr -o RSYNC.$stdBamId.$$.%J.stdout -R "rusage[mem=2]" -M 4 -n 1 "$RSYNC -a -L $_* $outdir/."";
$BSUB -q $queue -J AD.$bamID.$$ -cwd $outdir -e AD.$bamID.$$.%J.stderr -o AD.$bamID.$$.%J.stdout -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$PERL $GenotypeAllele -fmv $outdir/$AllStdFilterEntriesVcf -bam $outdir/$bamFile -rf $Reference -s $SAMTOOLS -o $outdir -of $alleleDepthMutationOut -mof $mpileUpMutationOut -bi $bamID -mmq $MAPQ -mbq $BASQ -q $queue -b $BEDTOOLS -bsub $BSUB -tos $typeOfSample[$index]"";
$BSUB
-q $queue
-cwd
$BSUB
-q $queue
-cwd
$BSUB
-q $queue
-cwd
$BSUB
-q $queue
-cwd
$BSUB
-q $queue
-cwd
$BSUB
-q $queue
-cwd
$BSUB -q $queue -cwd $outdir -J FilterSilentVariants.$$ -o FilterSilentVariants.$$.%J.stdout -e FilterSilentVariants.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$PERL $filterGenotypedVariants -i $outdir/$somaticMutIndelFile -h $HotspotMutations -ce $ClinicalExons -t $titleFile -dp_snv $dp_snv -ad_snv $ad_snv -vf_snv $vf_snv -dp_snvHS $dp_snvHS -ad_snvHS $ad_snvHS -vf_snvHS $vf_snvHS -dp_indel $dp_indel -ad_indel $ad_indel -vf_indel $vf_indel -dp_indelHS $dp_indelHS -ad_indelHS $ad_indelHS -vf_indelHS $vf_indelHS -occurrence $occurrencePercent -tn_ratio $TNfreqRatioThreshold -mt $MAFthreshold";
$BSUB
-q $queue
-cwd
$BSUB
-q $queue
-cwd
$BSUB
-q $queue
-cwd
-t $titleFile
-j $JAVA_1_7
-it $IGVtools"";
$BSUB -q $queue -cwd $outdir -J GenerateVCFfiles.$$ -o GenerateVCFfiles.$$.%J.stdout -e GenerateVCFfiles.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$PERL $createPatientVCFfile -v $somaticMutIndelFile -o $outdir -t $titleFile -j $JAVA_1_7 -it $IGVtools";
$BSUB
-q $queue
-cwd
-ct $coverageThreshold"";
$BSUB -q $queue -cwd $outdir -J GenerateCoverageFiles.$$ -o GenerateCoverageFiles.$$.%J.stdout -e GenerateCoverageFiles.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$PERL $createCoverageFiles -v $somaticMutIndelFile -o $outdir -nu $normalsUSed -t $titleFile -ss $sampleFile -id $intragenicLevelCNfile -gc $outdir/$geneCoverage -cn $geneLevelCNfile -gi $GeneIntervalAnn -ec $outdir/$exonCoverage -cc $outdir/$canonicalExonCoverage -ve $validatedExons -ce $ClinicalExons -ei $exonIntervalsFile -tf $translationFolder -ct $coverageThreshold";
$BSUB -q $queue -cwd $outdir -J Clipping.$id.$$ -o Clipping.$id.$$.%J.stdout -e Clipping.$id.$$.%J.stderr -R "rusage[mem=2]" -M 4 -n 1 "$PERL $TrimGalore --paired --gzip -q 1 --suppress_warn --stringency 3 -length 25 -o $outdir -a $adapter1 -a2 $adapter2 $file1 $file2"";
$BSUB -q $queue -cwd $outdir -J Clipping.$id.$$ -o Clipping.$id.$$.%J.stdout -e Clipping.$id.$$.%J.stderr -We 4:00 -R "rusage[mem=2]" -M 4 -n 1 "$PERL $TrimGalore --paired --gzip -q 1 --suppress_warn --stringency 3 -length 25 -o $outdir -a $adapter1 -a2 $adapter2 $file1 $file2";
$BSUB -q $queue -cwd $outdir -J bwaAln.$readType.$id.$$ -o bwaAln.$readType.$id.$$.%J.stdout -e bwaAln.$readType.$id.$$.%J.stderr -R "rusage[mem=5]" -M 8 -n 1 "$BWA aln -f $outFilename $Reference $file"";
$BSUB -q $queue -cwd $outdir -J bwaAln.$readType.$id.$$ -o bwaAln.$readType.$id.$$.%J.stdout -e bwaAln.$readType.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=5]" -M 8 -n 1 "$BWA aln -f $outFilename $Reference $file";
"$BSUB -q $queue -cwd $outdir -J bwaMem.$id.$$ -R "rusage[mem=10]" -M 40 -n 4 -o bwaMem.$id.$$.stdout -e bwaMem.$id.$$.stderr "$BWA mem -t 4 -PM -R '@RG\tID:$basename\tLB:$id\tSM:$sampleId\tPL:Illumina\tPU:$barcode\tCN:BergerLab_MSKCC' $Reference $fastq1 $fastq2 > $outFilename"";
$BSUB -q $queue -cwd $outdir -J bwaMem.$id.$$ -We 24:00 -R "rusage[mem=10]" -M 40 -n 4 -o bwaMem.$id.$$.stdout -e bwaMem.$id.$$.stderr "$BWA mem -t 4 -PM -R \'\@RG\tID:$basename\tLB:$id\tSM:$sampleId\tPL:Illumina\tPU:$barcode\tCN:BergerLab_MSKCC\' $Reference $fastq1 $fastq2 > $outFilename";
$BSUB -q $queue -cwd $outdir -J SortSam.$id.$$ -o SortSam.$id.$$.%J.stdout -e SortSam.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/AddOrReplaceReadGroups.jar I=$samFile O=$outFilename SO=coordinate RGID=$basename RGLB=$id RGPL=$platform RGPU=$barcode RGSM=$sampleId RGCN=MSKCC TMP_DIR=$TMPDIR COMPRESSION_LEVEL=0 CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT"";
$BSUB -q $queue -cwd $outdir -J SortSam.$id.$$ -o SortSam.$id.$$.%J.stdout -e SortSam.$id.$$.%J.stderr -We 6:00 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/AddOrReplaceReadGroups.jar I=$samFile O=$outFilename SO=coordinate RGID=$basename RGLB=$id RGPL=$platform RGPU=$barcode RGSM=$sampleId RGCN=MSKCC TMP_DIR=$TMPDIR COMPRESSION_LEVEL=0 CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT"`;
"$BSUB -q $queue -cwd $outdir -J FixMate.$id.$$ -o FixMate.$id.$$.%J.stdout -e FixMate.$id.$$.%J.stderr -R "rusage[mem=32]" -M 40 -n 4 "$JAVA_1_7 -Xmx24g -jar $PICARD/FixMateInformation.jar I=$bamFile O=$outFilename SO=coordinate TMP_DIR=$TMPDIR COMPRESSION_LEVEL=0 CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT"";
$BSUB -q $queue -cwd $outdir -J FixMate.$id.$$ -o FixMate.$id.$$.%J.stdout -e FixMate.$id.$$.%J.stderr -We 6:00 -R "rusage[mem=32]" -M 40 -n 4 "$JAVA_1_7 -Xmx24g -jar $PICARD/FixMateInformation.jar I=$bamFile O=$outFilename SO=coordinate TMP_DIR=$TMPDIR COMPRESSION_LEVEL=0 CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT";
"$BSUB -q $queue -cwd $outdir -J MD.$id.$$ -o MD.$id.$$.%J.stdout -e MD.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "/opt/common/CentOS_6/java/jdk1.8.0_31/bin/java -Xmx4g -jar /home/patelju1/software/picard-2.8.1.jar MarkDuplicates I=$bamFile O=$outFilename ASSUME_SORTED=true METRICS_FILE=$metricsFilename TMP_DIR=$TMPDIR COMPRESSION_LEVEL=0 CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES"";
$BSUB -q $queue -cwd $outdir -J MD.$id.$$ -o MD.$id.$$.%J.stdout -e MD.$id.$$.%J.stderr -We 6:00 -R "rusage[mem=8]" -M 12 -n 1 "/opt/common/CentOS_6/java/jdk1.8.0_31/bin/java -Xmx4g -jar /home/patelju1/software/picard-2.8.1.jar MarkDuplicates I=$bamFile O=$outFilename ASSUME_SORTED=true METRICS_FILE=$metricsFilename TMP_DIR=$TMPDIR COMPRESSION_LEVEL=0 CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES";
"`$BSUB -q $queue -cwd $outdir -J RTC.$jobName.$$ -o RTC.$jobName.$$.%J.stdout -e RTC.$jobName.$$.%J.stderr -R "rusage[mem=12]" -M 24 -n 2 "$JAVA_1_7 -Xmx20g -jar $GATK -T RealignerTargetCreator -I $outdir/$inputFiles -R $Reference -L $GeneInterval -o $outFilename --known $Mills_1000G_Indels"";
$BSUB -q $queue -cwd $outdir -J RTC.$jobName.$$ -o RTC.$jobName.$$.%J.stdout -e RTC.$jobName.$$.%J.stderr -We 24:00 -R "rusage[mem=12]" -M 24 -n 2 "$JAVA_1_7 -Xmx20g -jar $GATK -T RealignerTargetCreator -I $outdir/$inputFiles -R $Reference -L $GeneInterval -o $outFilename --known $Mills_1000G_Indels";
"$BSUB -q $queue -cwd $outdir -J IR.$id.$$ -o IR.$id.$$.%J.stdout -e IR.$id.$$.%J.stderr -R "rusage[mem=12]" -M 30 -n 2 "$JAVA_1_7 -Xmx20g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T IndelRealigner -I $file -R $Reference -targetIntervals $interval -o $outFilename -baq RECALCULATE -known $Mills_1000G_Indels"";
$BSUB -q $queue -cwd $outdir -J IR.$id.$$ -o IR.$id.$$.%J.stdout -e IR.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=12]" -M 30 -n 2 "$JAVA_1_7 -Xmx20g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T IndelRealigner -I $file -R $Reference -targetIntervals $interval -o $outFilename -baq RECALCULATE -known $Mills_1000G_Indels";
"$BSUB -q $queue -cwd $outdir -o BQSR1.$id.$$.%J.stdout -e BQSR1.$id.$$.%J.stderr -J BQSR1.$id.$$ -R "rusage[mem=3]" -M 36 -n 10 "$JAVA_1_7 -Xmx20g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T BaseRecalibrator -nct 10 -I $files -plots -R $Reference -knownSites $dbSNP -knownSites $Mills_1000G_Indels -rf BadCigar -o $outFilename1"";
$BSUB -q $queue -cwd $outdir -o BQSR1.$id.$$.%J.stdout -e BQSR1.$id.$$.%J.stderr -J BQSR1.$id.$$ -We 24:00 -R "rusage[mem=3]" -M 36 -n 10 "$JAVA_1_7 -Xmx20g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T BaseRecalibrator -nct 10 -I $files -plots -R $Reference -knownSites $dbSNP -knownSites $Mills_1000G_Indels -rf BadCigar -o $outFilename1";
"$BSUB -q $queue -cwd $outdir -R "rusage[mem=8]" -M 44 -n 5 -o BQSR1.$id.$$.%J.stdout -e BQSR1.$id.$$.%J.stderr -J BQSR1.$id.$$ "$JAVA_1_7 -Xmx30g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T BaseRecalibrator -I $files -R $Reference -knownSites $dbSNP -knownSites $Mills_1000G_Indels -rf BadCigar -o $outFilename1 -nct 3"";
$BSUB -q $queue -cwd $outdir -We 24:00 -R "rusage[mem=8]" -M 44 -n 5 -o BQSR1.$id.$$.%J.stdout -e BQSR1.$id.$$.%J.stderr -J BQSR1.$id.$$ "$JAVA_1_7 -Xmx30g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T BaseRecalibrator -I $files -R $Reference -knownSites $dbSNP -knownSites $Mills_1000G_Indels -rf BadCigar -o $outFilename1 -nct 3";
"$BSUB -q $queue -cwd $outdir -J PrintBQSR.$id.$$ -o PrintBQSR.$id.$$.%J.stdout -e PrintBQSR.$id.$$.%J.stderr -R "rusage[mem=8]" -M 30 -n 3 "$JAVA_1_7 -Xmx4g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T PrintReads -I $file -R $Reference -baq RECALCULATE -BQSR $BQSRtable -nct 8 -EOQ -o $outFilename"";
$BSUB -q $queue -cwd $outdir -J PrintBQSR.$id.$$ -o PrintBQSR.$id.$$.%J.stdout -e PrintBQSR.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -M 30 -n 3 "$JAVA_1_7 -Xmx4g -Djava.io.tmpdir=$TMPDIR -jar $GATK -T PrintReads -I $file -R $Reference -baq RECALCULATE -BQSR $BQSRtable -nct 8 -EOQ -o $outFilename";
"$BSUB -q $queue -cwd $outdir -J HSmetrics.$id.$$ -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/CalculateHsMetrics.jar I=$bamFile O=$HSmetricsFilename BI=$BaitInterval TI=$TargetInterval REFERENCE_SEQUENCE=$Reference PER_TARGET_COVERAGE=$perTargetCoverageFilename TMP_DIR=$TMPDIR VALIDATION_STRINGENCY=LENIENT"";
$BSUB -q $queue -cwd $outdir -J HSmetrics.$id.$$ -o HSmetrics.$id.$$.stdout -e HSmetrics.$id.$$.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/CalculateHsMetrics.jar I=$bamFile O=$HSmetricsFilename BI=$BaitInterval TI=$TargetInterval REFERENCE_SEQUENCE=$Reference PER_TARGET_COVERAGE=$perTargetCoverageFilename TMP_DIR=$TMPDIR VALIDATION_STRINGENCY=LENIENT"
"$BSUB -q $queue -cwd $outdir -J InsertSizeMetrics.$id.$$ -o InsertSizeMetrics.$id.$$.%J.stdout -e InsertSizeMetrics.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/CollectMultipleMetrics.jar I=$bamFile O=$basename PROGRAM=null PROGRAM=CollectInsertSizeMetrics ASSUME_SORTED=true TMP_DIR=$TMPDIR VALIDATION_STRINGENCY=LENIENT"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J InsertSizeMetrics.$id.$$ -o InsertSizeMetrics.$id.$$.%J.stdout -e InsertSizeMetrics.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/CollectMultipleMetrics.jar I=$bamFile O=$basename PROGRAM=null PROGRAM=CollectInsertSizeMetrics ASSUME_SORTED=true TMP_DIR=$TMPDIR VALIDATION_STRINGENCY=LENIENT";
$cmd =
"$BSUB -q $queue -cwd $outdir -J MeanQualityByCycle.$id.$$ -o MeanQualityByCycle.$id.$$.%J.stdout -e MeanQualityByCycle.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/CollectMultipleMetrics.jar I=$bamFile O=$basename PROGRAM=null PROGRAM=MeanQualityByCycle ASSUME_SORTED=true TMP_DIR=$TMPDIR VALIDATION_STRINGENCY=LENIENT"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J MeanQualityByCycle.$id.$$ -o MeanQualityByCycle.$id.$$.%J.stdout -e MeanQualityByCycle.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $PICARD/CollectMultipleMetrics.jar I=$bamFile O=$basename PROGRAM=null PROGRAM=MeanQualityByCycle ASSUME_SORTED=true TMP_DIR=$TMPDIR VALIDATION_STRINGENCY=LENIENT";
$BSUB -q $queue -cwd $outdir -w "post_done(InsertSizeMetrics.$id.$$) && post_done(MeanQualityByCycle.$id.$$)" -J NotifyMultipleMetrics.$id.$$ -e NotifyMultipleMetrics.$id.$$.%J.stderr -o NotifyMultipleMetrics.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J GeneCoverage.$id.$$ -o GeneCoverage.$id.$$.%J.stdout -e GeneCoverage.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $geneCoverage -L $GeneInterval -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J GeneCoverage.$id.$$ -o GeneCoverage.$id.$$.%J.stdout -e GeneCoverage.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $geneCoverage -L $GeneInterval -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput";
$cmd =
"$BSUB -q $queue -cwd $outdir -w "done(GeneCoverage.$id.$$)" -J ExonToGeneCov.$id.$$ -o ExonToGeneCov.$id.$$.%J.stdout -e ExonToGeneCov.$id.$$.%J.stderr -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$PERL $ExonToGenCov $geneCoverage.sample_interval_summary $GeneCoord > $geneCount"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -w "post_done(GeneCoverage.$id.$$)" -J ExonToGeneCov.$id.$$ -o ExonToGeneCov.$id.$$.%J.stdout -e ExonToGeneCov.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$PERL $ExonToGenCov $geneCoverage.sample_interval_summary $GeneCoord > $geneCount";
$BSUB -q $queue -cwd $outdir -w "post_done(ExonToGeneCov.$id.$$)" -J NotifyGeneCoverage.$id.$$ -e NotifyGeneCoverage.$id.$$.stderr -o NotifyGeneCoverage.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$QSUB -q $queue -V -wd $outdir -N GeneNomapqCoverage.$id.$$ -o GeneNomapqCoverage.$id.$$.stdout -e GeneNomapqCoverage.$id.$$.stderr -l h_vmem=8G,virtual_free=8G -pe smp 1 -b y '$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $gene_nomapqCoverage -L $GeneInterval -rf BadCigar -mmq 0 -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput'";
$logger->debug("COMMAND: $cmd");
$QSUB -q $queue -V -wd $outdir -N GeneNomapqCoverage.$id.$$ -o GeneNomapqCoverage.$id.$$.stdout -e GeneNomapqCoverage.$id.$$.stderr -l h_vmem=8G,virtual_free=8G -pe smp 1 -b y "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $gene_nomapqCoverage -L $GeneInterval -rf BadCigar -mmq 0 -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput";
$QSUB -q $queue -V -wd $outdir -hold_jid GeneNomapqCoverage.$id.$$ -N NotifyGeneNomapqCoverage.$id.$$ -e NotifyGeneNomapqCoverage.$id.$$.stderr -o NotifyGeneNomapqCoverage.$id.$$.stat -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J GeneNomapqCoverage.$id.$$ -o GeneNomapqCoverage.$id.$$.%J.stdout -e GeneNomapqCoverage.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $gene_nomapqCoverage -L $GeneInterval -rf BadCigar -mmq 0 -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J GeneNomapqCoverage.$id.$$ -o GeneNomapqCoverage.$id.$$.%J.stdout -e GeneNomapqCoverage.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $gene_nomapqCoverage -L $GeneInterval -rf BadCigar -mmq 0 -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput";
$BSUB -q $queue -cwd $outdir -w "post_done(GeneNomapqCoverage.$id.$$)" -J NotifyGeneNomapqCoverage.$id.$$ -e NotifyGeneNomapqCoverage.$id.$$.%J.stderr -o NotifyGeneNomapqCoverage.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J CanonicalExonCoverage.$id.$$ -o CanonicalExonCoverage.$id.$$.%J.stdout -e CanonicalExonCoverage.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $canonicalExonCoverage -L $canonicalExonIntervalsFile -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J CanonicalExonCoverage.$id.$$ -o CanonicalExonCoverage.$id.$$.%J.stdout -e CanonicalExonCoverage.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $canonicalExonCoverage -L $canonicalExonIntervalsFile -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput";
$BSUB -q $queue -cwd $outdir -w "post_done(CanonicalExonCoverage.$id.$$)" -J NotifyCanonicalExonCoverage.$id.$$ -e NotifyCanonicalExonCoverage.$id.$$.%J.stderr -o NotifyCanonicalExonCoverage.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J TilingCoverage.$id.$$ -o TilingCoverage.$id.$$.%J.stdout -e TilingCoverage.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $tilingCoverage -L $TilingInterval -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J TilingCoverage.$id.$$ -o TilingCoverage.$id.$$.%J.stdout -e TilingCoverage.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $tilingCoverage -L $TilingInterval -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput";
$BSUB -q $queue -cwd $outdir -w "post_done(TilingCoverage.$id.$$)" -J NotifyTilingCoverage.$id.$$ -e NotifyTilingCoverage.$id.$$.stderr -o NotifyTilingCoverage.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J TilingNomapqCoverage.$id.$$ -o TilingNomapqCoverage.$id.$$.%J.stdout -e TilingNomapqCoverage.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $tiling_nomapqCoverage -L $TilingInterval -rf BadCigar -mmq 0 -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J TilingNomapqCoverage.$id.$$ -o TilingNomapqCoverage.$id.$$.%J.stdout -e TilingNomapqCoverage.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $tiling_nomapqCoverage -L $TilingInterval -rf BadCigar -mmq 0 -mbq $BASQ -omitLocusTable -omitSampleSummary -omitBaseOutput";
$BSUB -q $queue -cwd $outdir -w "post_done(TilingNomapqCoverage.$id.$$)" -J NotifyTilingNomapqCoverage.$id.$$ -e NotifyTilingNomapqCoverage.$id.$$.stderr -o NotifyTilingNomapqCoverage.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J FingerPrint.$id.$$ -o FingerPrint.$id.$$.%J.stdout -e FingerPrint.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $fingerprintCounts -L $FingerPrintInterval -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitIntervals -baseCounts"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J FingerPrint.$id.$$ -o FingerPrint.$id.$$.%J.stdout -e FingerPrint.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T DepthOfCoverage -R $Reference -I $bamFile -o $fingerprintCounts -L $FingerPrintInterval -rf BadCigar -mmq $MAPQ -mbq $BASQ -omitLocusTable -omitSampleSummary -omitIntervals -baseCounts";
$cmd =
"$BSUB -q $queue -cwd $outdir -w "done(FingerPrint.$id.$$)" -J FingerPrintSummary.$id.$$ -o FingerPrint.$id.$$.%J.stdout -e FingerPrint.$id.$$.%J.stderr -R "rusage[mem=2]" -M 4 -n 1 "$PERL $FPGenotypesScript $fingerprintCounts $FP_genotypes > $fingerprintSummary"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -w "post_done(FingerPrint.$id.$$)" -J FingerPrintSummary.$id.$$ -o FingerPrint.$id.$$.%J.stdout -e FingerPrint.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$PERL $FPGenotypesScript $fingerprintCounts $FP_genotypes > $fingerprintSummary";
$BSUB -q $queue -cwd $outdir -w "post_done(FingerPrintSummary.$id.$$)" -J NotifyFingerPrintSummary.$id.$$ -e NotifyFingerPrintSummary.$id.$$.%J.stderr -o NotifyFingerPrintSummary.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $BSUB -q $queue -cwd $outdir -J CompileMetrics.$$ -o CompileMetrics.$$.%J.stdout -e CompileMetrics.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$PERL $CompileMetrics -i $allBams -t $titleFile -am $AllMetrics -cn $BestCopyNumber -ncn $NormVsNormCopyNumber -ce $exonIntervalsFile -gcb $GCBiasFile -snlo $StdNormalLoess_TM -snlon $StdNormalLoess_NVN -gia $GeneIntervalAnn -tia $TilingIntervalAnn -ln $LoessNormalization -o $outdir -q $queue -bsub $BSUB -p $PERL -rh $RHOME -rl $RLIBS -ms $GenerateMetricsFilesScript";
$BSUB -q $queue -cwd $outdir -w "post_done(CompileMetrics.$$)" -J NotifyCM.$$ -e NotifyCM.$$.%J.stderr -o NotifyCM.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J UGM.$id.$$ -o UGM.$id.$$.%J.stdout -e UGM.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T UnifiedGenotyper -R $Reference -I $bamFile -o $outFilename1 -rf BadCigar --dbsnp $dbSNP -glm SNP -dcov 50000 -L $GeneInterval"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J UGM.$id.$$ -o UGM.$id.$$.%J.stdout -e UGM.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T UnifiedGenotyper -R $Reference -I $bamFile -o $outFilename1 -rf BadCigar --dbsnp $dbSNP -glm SNP -dcov 50000 -L $GeneInterval";
$cmd =
"$BSUB -q $queue -cwd $outdir -J UGI.$id.$$ -o UGI.$id.$$.%J.stdout -e UGI.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T UnifiedGenotyper -R $Reference -I $bamFile -o $outFilename2 -rf BadCigar --dbsnp $dbSNP -glm INDEL -dcov 50000 -L $GeneInterval"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J UGI.$id.$$ -o UGI.$id.$$.%J.stdout -e UGI.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_7 -Xmx4g -jar $GATK -T UnifiedGenotyper -R $Reference -I $bamFile -o $outFilename2 -rf BadCigar --dbsnp $dbSNP -glm INDEL -dcov 50000 -L $GeneInterval";
$BSUB -q $queue -cwd $outdir -w "post_done(UGM.$id.$$) && post_done(UGI.$id.$$)" -J NotifyUG.$id.$$ -e NotifyUG.$id.$$.%J.stderr -o NotifyUG.$id.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh";
"$BSUB -q $queue -cwd $outdir -J MuTect.$id.$$ -o MuTect.$id.$$.%J.stdout -e MuTect.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_6 -Xmx4g -jar $Mutect -T MuTect --input_file:normal $normalBamFile --input_file:tumor $tumorBamFile --reference_sequence $Reference --dbsnp $dbSNP --cosmic $COSMIC -o $MutationVerboseOutFilename -vcf $MutationOutFilename --enable_extended_output -dcov 50000 -rf BadCigar -rf MappingQuality -mmq $MAPQ"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J MuTect.$id.$$ -o MuTect.$id.$$.%J.stdout -e MuTect.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_6 -Xmx4g -jar $Mutect -T MuTect --input_file:normal $normalBamFile --input_file:tumor $tumorBamFile --reference_sequence $Reference --dbsnp $dbSNP --cosmic $COSMIC -o $MutationVerboseOutFilename -vcf $MutationOutFilename --enable_extended_output -dcov 50000 -rf BadCigar -rf MappingQuality -mmq $MAPQ";
"$BSUB -q $queue -cwd $outdir -J SID.$id.$$ -o SID.$id.$$.%J.stdout -e SID.$id.$$.%J.stderr -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_6 -Xmx4g -jar $GATK_SomaticIndel -T SomaticIndelDetector -R $Reference -I:normal $normalBamFile -I:tumor $tumorBamFile -filter 'T_COV<10||N_COV<4||T_INDEL_F<0.0001||T_INDEL_CF<0.7' -verbose $IndelVerboseOutFilename -o $IndelOutFilename -refseq $Refseq --maxNumberOfReads 100000 -rf DuplicateRead -rf FailsVendorQualityCheck -rf NotPrimaryAlignment -rf BadMate -rf MappingQualityUnavailable -rf UnmappedRead -rf BadCigar -rf MappingQuality -mmq $MAPQ -L $targetFile"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J SID.$id.$$ -o SID.$id.$$.%J.stdout -e SID.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=8]" -M 12 -n 1 "$JAVA_1_6 -Xmx4g -jar $GATK_SomaticIndel -T SomaticIndelDetector -R $Reference -I:normal $normalBamFile -I:tumor $tumorBamFile -filter 'T_COV<10||N_COV<4||T_INDEL_F<0.0001||T_INDEL_CF<0.7' -verbose $IndelVerboseOutFilename -o $IndelOutFilename -refseq $Refseq --maxNumberOfReads 100000 -rf DuplicateRead -rf FailsVendorQualityCheck -rf NotPrimaryAlignment -rf BadMate -rf MappingQualityUnavailable -rf UnmappedRead -rf BadCigar -rf MappingQuality -mmq $MAPQ -L $targetFile";
"$BSUB -q $queue -cwd $outdir -J PID.$id.$$ -o PID.$id.$$.%J.stdout -e PID.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -R "rusage[iounits=0]" -M 12 -n 1 "$PYTHON $PindelWrapper -i $pconfig -pId $tFileId -t 5 -r $Reference -p $PINDELBIN -chr ALL -q $queue -bsub $BSUB -o $outdir -op $tFileId"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J PID.$id.$$ -o PID.$id.$$.%J.stdout -e PID.$id.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -R "rusage[iounits=0]" -M 12 -n 1 "$PYTHON $PindelWrapper -i $pconfig -pId $tFileId -t 5 -r $Reference -p $PINDELBIN -chr ALL -q $queue -bsub $BSUB -o $outdir -op $tFileId";
"$BSUB -q $queue -cwd $outdir -J FilterMuTect.$id.$$ -o FilterMuTect.$id.$$.%J.stdout -e FilterMuTect.$id.$$.%J.stderr -R "rusage[mem=2]" -M 4 -n 1 "$PERL $filter_Mutect -t $outdir/$MutationVerboseFilename -v $outdir/$MutationVcfFilename -s $tFileId -o $outdir -dp $dp_MutectStdFilter -ad $ad_MutectStdFilter -vf $vf_MutectStdFilter -tnr $TNfreqRatio_MutectStdFilter"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J FilterMuTect.$id.$$ -o FilterMuTect.$id.$$.%J.stdout -e FilterMuTect.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$PERL $filter_Mutect -t $outdir/$MutationVerboseFilename -v $outdir/$MutationVcfFilename -s $tFileId -o $outdir -dp $dp_MutectStdFilter -ad $ad_MutectStdFilter -vf $vf_MutectStdFilter -tnr $TNfreqRatio_MutectStdFilter";
"$BSUB -q $queue -cwd $outdir -J FilterSID.$id.$$ -o FilterSID.$id.$$.%J.stdout -e FilterSID.$id.$$.%J.stderr -R "rusage[mem=2]" -M 4 -n 1 "$PERL $filter_SomaticIndel -t $outdir/$IndelVerboseFilename -v $outdir/$IndelVcfFilename -s $tFileId -o $outdir -dp $dp_SomIndelStdFilter -ad $ad_SomIndelStdFilter -vf $vf_SomIndelStdFilter -tnr $TNfreqRatio_SomIndelStdFilter"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J FilterSID.$id.$$ -o FilterSID.$id.$$.%J.stdout -e FilterSID.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$PERL $filter_SomaticIndel -t $outdir/$IndelVerboseFilename -v $outdir/$IndelVcfFilename -s $tFileId -o $outdir -dp $dp_SomIndelStdFilter -ad $ad_SomIndelStdFilter -vf $vf_SomIndelStdFilter -tnr $TNfreqRatio_SomIndelStdFilter";
"$BSUB -q $queue -cwd $outdir -J FilterPID.$id.$$ -o FilterPID.$id.$$.%J.stdout -e FilterPID.$id.$$.%J.stderr -R "rusage[mem=2]" -M 4 -n 1 "$PYTHON $filter_Pindel -i $outdir/$PindelVcfFilename -tsn $tFileId -o $outdir -dp $dp_SomIndelStdFilter -ad $ad_SomIndelStdFilter -vf $vf_SomIndelStdFilter -tnr $TNfreqRatio_SomIndelStdFilter -min $Pindel_Min_Indel_Len -max $Pindel_Max_Indel_Len -o $outdir"";
$logger->debug("COMMAND: $cmd");
$BSUB -q $queue -cwd $outdir -J FilterPID.$id.$$ -o FilterPID.$id.$$.%J.stdout -e FilterPID.$id.$$.%J.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$PYTHON $filter_Pindel -i $outdir/$PindelVcfFilename -tsn $tFileId -o $outdir -dp $dp_SomIndelStdFilter -ad $ad_SomIndelStdFilter -vf $vf_SomIndelStdFilter -tnr $TNfreqRatio_SomIndelStdFilter -min $Pindel_Min_Indel_Len -max $Pindel_Max_Indel_Len -o $outdir";
"$BSUB -q $queue -cwd $BSUB -q $queue -cwd $outdir -J RunSV.$$ -o RunSV.$$.%J.stdout -e RunSV.$$.%J.stderr -We 24:00 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$PERL $SVpipeline -c $sv_config_file -d $datadir -o $outdir";
"$BSUB -q $queue -cwd $outdir -J RunFindCoveredInterval_IR.$i.$$ -o RunFindCoveredInterval_IR.$i.$$.%J.stdout -e RunFindCoveredInterval.$i.$$.%J.stderr -R "rusage[mem=8]" -R "rusage[iounits=0]" -M 12 -n 1 "$PYTHON $FindCoveredIntervals -i $inputFiles -of $targetFilePrefix -t 4 -r $Reference -g $GATK -j $JAVA_1_7 -q $queue -bsub $BSUB -o $outdir"";
$BSUB -q $queue -cwd $outdir -J RunFindCoveredInterval_IR.$i.$$ -o RunFindCoveredInterval_IR.$i.$$.%J.stdout -e RunFindCoveredInterval.$i.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -R "rusage[iounits=0]" -M 12 -n 1 "$PYTHON $FindCoveredIntervals -i $inputFiles -of $targetFilePrefix -t 4 -r $Reference -g $GATK -j $JAVA_1_7 -q $queue -bsub $BSUB -o $outdir";
"$BSUB -q $queue -cwd $outdir -J RunFindCoveredInterval_IR.$i.$$ -o RunFindCoveredInterval_IR.$i.$$.%J.stdout -e RunFindCoveredInterval.$i.$$.%J.stderr -R "rusage[mem=8]" -R "rusage[iounits=0]" -M 12 -n 1 "$PYTHON $FindCoveredIntervals -i $inputFiles -of $targetFilePrefix -t 4 -r $Reference -g $GATK -j $JAVA_1_7 -q $queue -bsub $BSUB -o $outdir"";
$BSUB -q $queue -cwd $outdir -J RunFindCoveredInterval_IR.$i.$$ -o RunFindCoveredInterval_IR.$i.$$.%J.stdout -e RunFindCoveredInterval.$i.$$.%J.stderr -We 24:00 -R "rusage[mem=8]" -R "rusage[iounits=0]" -M 12 -n 1 "$PYTHON $FindCoveredIntervals -i $inputFiles -of $targetFilePrefix -t 4 -r $Reference -g $GATK -j $JAVA_1_7 -q $queue -bsub $BSUB -o $outdir";
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