diff --git a/perl/runReleaseSanityCheck.pl b/perl/runReleaseSanityCheck.pl new file mode 100755 index 000000000..990198ad7 --- /dev/null +++ b/perl/runReleaseSanityCheck.pl @@ -0,0 +1,70 @@ +#!/usr/bin/perl + +# Usage:runReleaseSanityCheck [-sting \$dry, + "sting=s" => \$junit); + +$command_prefix = "java -Xmx4096m -jar $sting -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"; + +$random_number = rand(); +$tmp_bam = "/tmp/$random_number.bam"; + +print "Executing CountCovariatesWholeExome..."; +$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -standard -OQ -recalFile /dev/null -XL chr1:1,000,000-247179187"; +run($command, $dry); + +print "Executing CountCovariatesWholeGenome..."; +$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:1,900,000-2,000,000 -standard -OQ -recalFile /dev/null"; +run($command, $dry); + +print "Executing TableRecalibratorWholeExome..."; +$command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -OQ -recalFile /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.recal.csv -outputBam $tmp_bam -XL chr1:1,000,000-247179187"; +run($command, $dry); + +print "Executing TableRecalibratorWholeGenome..."; +$command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:1,950,000-2,000,000 -OQ -recalFile /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.recal.csv -outputBam $tmp_bam"; +run($command, $dry); + +print "Executing IndelRealignerWholeExome..."; +$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L chr1:900,000-1,000,000 -compress 1 -sort NO_SORT -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.realigner.intervals -O $tmp_bam"; +run($command, $dry); + +print "Executing IndelRealignerWholeGenome..."; +$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:975,000-1,000,000 -compress 1 -sort NO_SORT -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.realigner.intervals -O $tmp_bam"; +run($command, $dry); + +print "Executing UnifiedGenotyperWholeExome..."; +$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null -XL chr1:1,500,000-247179187"; +run($command, $dry); + +print "Executing UnifiedGenotyperWholeGenome..."; +$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:750,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null"; +run($command, $dry); + +print "Executing UnifiedGenotyperWholeGenomeMultithreaded..."; +$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:500,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null -nt 4"; +run($command, $dry); + +unlink $tmp_bam; + +sub run { + + $command = $_[0]; + $dry = $_[1]; + + local $start = time; + + if ($dry) { + print "$command\n"; + } else { + system($command); + } + + $total_time = time - $start; + print " [$total_time sec]\n"; +}