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updated to deal with new cleaner options 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3728 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-07 17:06:00 +00:00
parent b934cc7554
commit 2ac74a862d
1 changed files with 2 additions and 2 deletions
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4
perl/runReleaseSanityCheck.pl
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@ -31,11 +31,11 @@ $command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK
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";
$command = "$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 $tmp_bam";
run($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";
$command = "$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 $tmp_bam";
run($command, $dry);
print "Executing UnifiedGenotyperWholeExome...";