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some fixes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1622 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-15 01:35:36 +00:00
parent fb254759cb
commit 76838673e5
3 changed files with 15 additions and 11 deletions
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16
perl/1kgScripts/runCleaningPipeline.pl
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@ -63,33 +63,37 @@ if ($inject) {
} else {
$cleanedBam = "$outputBam";
}
$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -compress 1";
$command = "bsub -q $queue -o $outputBam.cleaner.script1 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -compress 1";
if ($inject) {
$command .= " -cleanedOnly\" -j $outputBam.cleaned";
} else {
$command .= "\" -j $jobName";
}
$command .= " -o $cleanedBam -oarg O -wait $outputBam.merged -q $queue -bam -i $mergedIntervals -n 50";
$command .= " -o $cleanedBam -oarg O -q $queue -bam -i $mergedIntervals -n 50";
if ($dry) {
$command .= " -dry";
print "$command\n";
} else {
system($command);
}
system($command);
my $snpsFile = $badsnps;
if (!$snpsFile) {
$snpsFile = "$outputBam.badsnps";
}
$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\"";
$command = "bsub -q $queue -o $outputBam.cleaner.script2 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\"";
if ($inject) {
$command .= " -j $outputBam.cleaned";
} else {
$command .= " -j $jobName";
}
$command .= "\" -o $snpsFile -oarg snps -wait $outputBam.merged -q $queue -i $mergedIntervals -n 50";
$command .= " -o $snpsFile -oarg snps -q $queue -i $mergedIntervals -n 50";
if ($dry) {
$command .= " -dry";
print "$command\n";
} else {
system($command);
}
system($command);
if ($inject) {
my $bam = "$outputBam";

6
perl/1kgScripts/runPilot2Pipeline.pl
View File

@ -15,7 +15,7 @@ my $queue = "gsa";
my $sting = "/humgen/gsa-scr1/ebanks/Sting";
GetOptions( "i=s" => \$inputDir,
"odir=s" => \$outputDir,
"o=s" => \$outputDir,
"q:s" => \$queue,
"dry!" => \$dry,
"sting:s" => \$sting );
@ -44,7 +44,7 @@ foreach my $sample (@samples) {
my $inputBamSLX = "$inputDir/$sample.pilot2.SLX.bam";
my $outputHeadSLX = "$outputDir/$sample.SLX";
my $outputBamSLX = "$outputHeadSLX.bam";
my $badsnpsSLX = "$outputDir/$outputBamSLX.badsnps";
my $badsnpsSLX = "$outputBamSLX.badsnps";
clean($inputBamSLX, $outputBamSLX, $queue, $sting, $dry, $badsnpsSLX);
call("-I $outputBamSLX", $outputHeadSLX, $queue, $sting, $dry, "$inputBamSLX.cleaningpipeline", $sample, $badsnpsSLX, $DoC_slx{$sample}, $MQ_hash{"SLX"});
@ -52,7 +52,7 @@ foreach my $sample (@samples) {
my $inputBamSOLID = "$inputDir/$sample.pilot2.SOLID.bam";
my $outputHeadSOLID = "$outputDir/$sample.SOLID";
my $outputBamSOLID = "$outputHeadSOLID.bam";
my $badsnpsSOLID = "$outputDir/$outputBamSOLID.badsnps";
my $badsnpsSOLID = "$outputBamSOLID.badsnps";
clean($inputBamSOLID, $outputBamSOLID, $queue, $sting, $dry, $badsnpsSOLID);
call("-I $outputBamSOLID", $outputHeadSOLID, $queue, $sting, $dry, "$inputBamSOLID.cleaningpipeline", $sample, $badsnpsSOLID, $DoC_solid{$sample}, $MQ_hash{"SOLID"});

4
perl/1kgScripts/runPilotPipelines.sh
View File

@ -1,2 +1,2 @@
#perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot1Pipeline.pl -i /humgen/gsa-hphome1/projects/1kg_pilot1/mergedBamsByPopulation -o /broad/hptmp/ebanks/1kg_pilot1/cleaned -dry
perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot2Pipeline.pl -i /broad/1KG/DCC_merged/freeze5.2 -o /broad/hptmp/ebanks/1kg_pilot2/cleaned -dry
#perl /humgen/gsa-scr1/ebanks/Sting_STABLE/perl/1kgScripts/runPilot1Pipeline.pl -i /humgen/gsa-hphome1/projects/1kg_pilot1/mergedBamsByPopulation -o /broad/hptmp/ebanks/1kg_pilot1/cleaned -sting /humgen/gsa-scr1/ebanks/Sting_STABLE -dry
perl /humgen/gsa-scr1/ebanks/Sting_STABLE/perl/1kgScripts/runPilot2Pipeline.pl -i /broad/1KG/DCC_merged/freeze5.2 -o /broad/hptmp/ebanks/1kg_pilot2/cleaned -sting /humgen/gsa-scr1/ebanks/Sting_STABLE