BENCHMARK RECIPE Deploying GATK Best Practices Pipeline Below are the scripts files accompanying and as documented in the Infrastructure for Deploying GATK Best Practices Pipeline paper. ____________________________________________________________________________ GATK Best Practices Pipeline_README The following scripts are designed to take the same arguments to keep it consistent for running tests. For single threaded baseline analysis with no optimizations, run the data_colletion_gatk_best_practices_pl script with NumThreads as “1”. For both thread level and process level parallelism analysis, use the data_collection_gatk_best_practices_optimized.pl script with NumThreads as proposed in the paper. ____________________________________________________________________________________________ Data Collection Script for GATK Best Practices Pipeline (wgs_end2end_data_collection_gatk_best_practices.pl) #!/usr/bin/perl if (scalar(@ARGV) < 5) { die("Usage: SampleName NumThreads InputDataDirectory TempOutputDirectory profiling \n[if profiling is enabled, then the following is required]: collectstatspath interval stats \n"); } my $sample = $ARGV[0]; my $numThreads = $ARGV[1]; my $inDataDir = $ARGV[2]; my $tmpDir = "".$ARGV[3]; my $profiling = $ARGV[4]; #by default profiling is turned ON if invoked from the workflow profiler # arguments for collect_stats my $collectstatspath = $ARGV[5]; my $interval = $ARGV[6]; # by default sampling interval is 30s from the workflow profiler. my $stats = $ARGV[7]; #my $numLanes =$ARGV[1]; my $called = "$0 @ARGV"; my $numLanes = 0; my $sampleprefix = $sample.'_'.$numThreads.'T'; 1 BENCHMARK RECIPE Data Collection Script for GATK Best Practices Pipeline (cont) # INPUT FASTQ FILES #OTHER FORMATS FOR FQ: "_1.fastq.gz; #"_1.fastq"; my $fqFile1, $fqFile2; $fqFile1 = $inDataDir.$sample."_1.fq"; $fqFile2 = $inDataDir.$sample."_2.fq"; # Pipeline executables and its directories ### SPECIFY PATH IN THE VARIABLES BELOW ### my $toolsDir = '/PATH/TO/TOOLS_DIR'; my $homosapiensrefgenomeDir = '/PATH/TO/REF'; # TOOLS my $bwaDir = "$toolsDir/bwa"; my $bwa = "$bwaDir/bwa"; my $gatkDir = "$toolsDir/gatk-protected/target"; my $gatk = "$gatkDir/GenomeAnalysisTK.jar"; my $picardDir ="$toolsDir/picard/dist"; my $picard = "$picardDir/picard.jar"; # HOMOSAPIENSREFGENOME my $refgenomeFastaFile = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.fasta"; my $refgenomeBwtFile = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.fasta.bwt"; my $dbSNPvcf = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.dbsnp.vcf"; my $dbSNPindel = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.known_indels.vcf"; # EXOME TARGET INTERVALS my $exome_targets_intervals = "$homosapiensrefgenomeDir/nexterarapidcapture_exome_uniqueintervals.bed"; unless(-d $inDataDir) { die("Error: The InputDataDirectory $inDataDir doesn't exist\n"); } unless(-d $tmpDir) { die("Error: The TempOutputDirectory $tmpDir doesn't exist\n"); } # Output file names for each stage of the pipeline my $baseName = $sample; my $baseNameLane = $baseName.'_'.$numLanes.'L_'.$numThreads.'T'; my $bwamem_samFile = $tmpDir.$baseNameLane.".sam"; my $sort_bamFile = $tmpDir.$baseName."_sorted.bam"; my $duplicateMetricsFile = $tmpDir.$baseName."_dup.metrics"; my $bamDupRemFile = $tmpDir.$baseName."_dupRem.bam"; my $bamRealignFile = $tmpDir.$baseName."_realign.bam"; my $realnInterval = $tmpDir.$baseName."_realn.intervals"; my $finalBam = $tmpDir.$baseName."_final.bam"; my $HCvcf = $tmpDir.$baseName."_HaplotypeCaller.vcf"; my $genomeImportFile = $refgenomeFastaFile.".fai"; #ADD the relevant platform my $readGroupHeader = "\@RG\\tID:$baseNameLane\\tLB:$baseName\\tSM:$baseName\\tPL:PLATFORM"; my $recalOut = $tmpDir .$baseName."_recal.grp"; my $dryRun = 0; my $pwd = `pwd`; chomp $pwd; my $host = `hostname`; chomp $host; my $uname = `whoami`; chomp $uname; my $runningTime = time; my $commandsfile = $tmpDir.$uname."_".$sampleprefix."_processing.log"; my $outputfile = $tmpDir.$uname."_".$sampleprefix."_output.log"; open(LOG,">$commandsfile"); 2 BENCHMARK RECIPE Data Collection Script for GATK Best Practices Pipeline (cont) print LOG "#$called (version $version) in $pwd on $host.\n"; print LOG "#Started at ".`date +"%F %T"`."\n"; print LOG "#temporary files created in $tmpDir\n"; my $procTime = time; my $procFlag = 0; sub run_and_log { my $command = $_[0]; my $execute = !$dryRun; my $exitValue = 0; #a command we don't run is considered successful my $redirect; if (@_ >1){ $execute=!$_[1]; } #several of the programs like to output to STDERR, so we link that to log file $redirect = "1>>$outputfile 2>&1"; #that is because we redirect STDOUT in many cases, so let's not mess with it. $redirect = "2>>$outputfile" if $command =~ m/>/; # $redirect = "" if $command =~ m/>/; $command = $command." ".$redirect; if ($procFlag == 0){ $procFlag++; } else { $procTime = time - $procTime; printf LOG "#Processing Time %02d:%02d:%02d\n",int($procTime /3600),int(($procTime % 3600) /60),int($procTime %60); $procTime = time; } print LOG "#not run\n" if !$execute; print LOG "#".`date +"%F %T"`; print LOG $command."\n"; $exitValue = system($command) if $execute; #necessary if we use `` instead of system() #$exitValue = $? >>8; ##If the command failed, we want to stop it here. if ($exitValue != 0){ my $error = "Command failed with return value $exitValue : $command \n"; print LOG $error; close LOG; die $error; } } sub Start_profiling { my ($tag) = @_; if ($profiling) { system("$collectstatspath $stats -d $interval -td $tmpDir -n $sampleprefix -tag $tag -l 5 -u 1 -s 600 &"); } } sub Stop_Profiling { 3 BENCHMARK RECIPE Data Collection Script for GATK Best Practices Pipeline (cont) if ($profiling) { system("$collectstatspath --kill-all"); } } my $stage_tag=BwaMem; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "$bwa mem -t $numThreads -Ma -R \'$readGroupHeader\' $refgenomeFastaFile $fqFile1 $fqFile2 > $bwamem_samFile"; Stop_Profiling(); sleep(60); my $stage_tag=SortSam; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "java -Xmx8g -jar $picard SortSam I=$bwamem_samFile O=$sort_bamFile SO=coordinate CREATE_INDEX=true"; Stop_Profiling(); sleep(60); my $stage_tag=MarkDuplicates; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "java -Xmx8g -jar $picard MarkDuplicates I=$sort_bamFile O=$bamDupRemFile M=$duplicateMetricsFile CREATE_INDEX=true TMP_DIR=$tmpDir"; Stop_Profiling(); sleep(60); my $stage_tag=RealignerTargetCreator; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "java -Xmx8g -jar $gatk -T RealignerTargetCreator -nt $numThreads -R $refgenomeFastaFile -o $realnInterval -known:indels,vcf $dbSNPindel -I $bamDupRemFile"; Stop_Profiling(); sleep(60); my $stage_tag=IndelRealigner; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "java -Xmx8g -Djava.io.tmpdir=$tmpDir -jar $gatk -T IndelRealigner -R $refgenomeFastaFile - targetIntervals $realnInterval -known:indels,vcf $dbSNPindel -I $bamDupRemFile -o $bamRealignFile -- filter_bases_not_stored"; Stop_Profiling(); sleep(60); my $stage_tag=BaseRecalibrator; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "java -Xmx4g -jar $gatk -T BaseRecalibrator -I $bamRealignFile -R $refgenomeFastaFile - knownSites:mask,vcf $dbSNPvcf -o $recalOut"; Stop_Profiling(); sleep(60); 4 BENCHMARK RECIPE Stages of GATK Best Practices Pipeline (cont) my $stage_tag=PrintReads; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "java -Xmx8g -jar $gatk -T PrintReads -R $refgenomeFastaFile -I $bamRealignFile -BQSR $recalOut -o $finalBam"; Stop_Profiling(); sleep(60); my $stage_tag=HaplotypeCaller; Start_profiling($stage_tag); print "$stage_tag\n"; run_and_log "java -Xmx8g -jar $gatk -T HaplotypeCaller -R $refgenomeFastaFile -I $finalBam -o $HCvcf -ERC GVCF --variant_index_type LINEAR --variant_index_parameter 128000"; Stop_Profiling(); sleep(60); $runningTime = time - $runningTime; printf LOG "#done in %02d:%02d:%02d\n",int($runningTime /3600),int(($runningTime % 3600) /60),int($runningTime %60); exit 0; Data Collection Script for GATK Best Practices Pipeline Optimized (wgs_end2end_data_collection_gatk_best_practices_optimized.pl) #!/usr/bin/perl if (scalar(@ARGV) < 5) { die("Usage: SampleName NumThreads InputDataDirectory TempOutputDirectory profiling \n[if profiling is enabled, then the following is required]: collectstatspath interval stats \n"); } my $sample = $ARGV[0]; my $numThreads = $ARGV[1]; my $inDataDir = $ARGV[2]; my $tmpDir = "".$ARGV[3]; my $profiling = $ARGV[4]; #by default profiling is turned ON if invoked from the workflow profiler # arguments for collect_stats my $collectstatspath = $ARGV[5]; my $interval = $ARGV[6]; # by default sampling interval is 30s from the workflow profiler. my $stats = $ARGV[7]; #my $numLanes =$ARGV[1]; my $called = "$0 @ARGV"; my $numLanes = 0; my $sampleprefix = $sample.'_'.$numThreads.'T'; 5 BENCHMARK RECIPE Data Collection Script for GATK Best Practices Pipeline Optimized (cont) # INPUT FASTQ FILES #OTHER FORMATS FOR FQ: "_1.fastq.gz; #"_1.fastq"; my $fqFile1, $fqFile2; $fqFile1 = $inDataDir.$sample."_1.fq"; $fqFile2 = $inDataDir.$sample."_2.fq"; # Pipeline executables and its directories ### SPECIFY PATH IN THE VARIABLES BELOW ### my $toolsDir = '/PATH/TO/TOOLS_DIR'; #SCALA_SCRIPTS: Scripts to be passed to Queue.jar my $QueueBroadBestPracticesDir = '/PATH/TO/SCALA_SCRIPTS'; my $homosapiensrefgenomeDir = '/PATH/TO/REF'; # TOOLS my $bwaDir = "$toolsDir/bwa"; my $bwa = "$bwaDir/bwa"; my $gatkDir = "$toolsDir/gatk-protected/target"; my $gatk = "$gatkDir/GenomeAnalysisTK.jar";