75 lines
4.3 KiB
Perl
Executable File
75 lines
4.3 KiB
Perl
Executable File
#!/usr/bin/perl
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# Usage:runReleaseSanityCheck [-sting <path to GATK jar>] [-dry]
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use Getopt::Long;
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$dry;
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$sting = "/humgen/gsa-scr1/ebanks/Sting_dev/dist/GenomeAnalysisTK.jar";
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GetOptions( "dry!" => \$dry,
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"sting=s" => \$sting);
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$command_prefix = "java -Xmx4096m -jar $sting -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -l OFF";
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$random_number = rand();
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$tmp_bam = "/tmp/$random_number.bam";
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print "Executing DepthOfCoverage...";
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$command = "$command_prefix -T DepthOfCoverage -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L chr1:10000000-10100000 -o /dev/null";
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run($command, $dry);
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print "Executing CountCovariatesWholeExome...";
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$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -standard -OQ -recalFile /dev/null -XL chr1:1,000,000-247179187";
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run($command, $dry);
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print "Executing CountCovariatesWholeGenome...";
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$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -L chr1:1,900,000-2,000,000 -standard -OQ -recalFile /dev/null";
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run($command, $dry);
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print "Executing TableRecalibratorWholeExome...";
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$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 --out $tmp_bam -XL chr1:1,000,000-247179187";
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run($command, $dry);
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print "Executing TableRecalibratorWholeGenome...";
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$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 --out $tmp_bam";
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run($command, $dry);
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print "Executing IndelRealignerWholeExome...";
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$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 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.realigner.intervals -o $tmp_bam";
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run($command, $dry);
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print "Executing IndelRealignerWholeGenome...";
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$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 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.realigner.intervals -o $tmp_bam";
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run($command, $dry);
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print "Executing UnifiedGenotyperWholeExome...";
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$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null -XL chr1:1,500,000-247179187";
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run($command, $dry);
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print "Executing UnifiedGenotyperWholeGenome...";
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$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:750,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null";
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run($command, $dry);
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print "Executing UnifiedGenotyperWholeGenomeMultithreaded...";
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$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:500,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null -nt 4";
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run($command, $dry);
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unlink $tmp_bam;
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sub run {
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$command = $_[0];
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$dry = $_[1];
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local $start = time;
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if ($dry) {
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print "$command\n";
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} else {
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system($command);
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}
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$total_time = time - $start;
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print " [$total_time sec]\n";
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}
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