109 lines
3.9 KiB
Perl
Executable File
109 lines
3.9 KiB
Perl
Executable File
#!/usr/bin/perl -w
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use strict;
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use Getopt::Long;
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sub usage {
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print "Usage: perl runPilot2Pipeline.pl\n\t-i <input dir>\n\t-o <output directory>\n\t[-sting Sting dir]\n\t[-q farm queue; default:gsa]\n\t[-dry]\n";
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exit(1);
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}
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my $inputDir = undef;
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my $outputDir = undef;
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my $dry;
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my $queue = "gsa";
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my $sting = "/humgen/gsa-scr1/ebanks/Sting";
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GetOptions( "i=s" => \$inputDir,
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"o=s" => \$outputDir,
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"q:s" => \$queue,
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"dry!" => \$dry,
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"sting:s" => \$sting );
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usage() if ( !$inputDir || !$outputDir );
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my @samples = ("NA19238","NA19239","NA19240","NA12878","NA12891","NA12892");
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# Official genome-wide Depth of Coverage tables for pilot 2, freeze 5:
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# NA12878 NA12891 NA12892 NA19238 NA19239 NA19240
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# 454: 36 18
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# SLX: 82 91 70 56 68 86
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# SOLID: 37 64
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# 454+SLD: 64 77
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# ALL: 138 150
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my %DoC_454 = ( "NA12878" => 36, "NA19240" => 18 );
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my %DoC_slx = ( "NA12878" => 82, "NA12891" => 91, "NA12892" => 70,"NA19238" => 56, "NA19239" => 68, "NA19240" => 86 );
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my %DoC_solid = ( "NA12878" => 37, "NA19240" => 64 );
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my %DoC_454solid = ( "NA12878" => 64, "NA19240" => 77 );
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my %DoC_all = ( "NA12878" => 138, "NA19240" => 150 );
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my %MQ_hash = ( "SLX" => 100, "SOLID" => 5, "454" => 5, "454SOLID" => 10, "ALL" => 110 );
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foreach my $sample (@samples) {
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my $inputBamSLX = "$inputDir/$sample.pilot2.SLX.bam";
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my $outputHeadSLX = "$outputDir/$sample.SLX";
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my $outputBamSLX = "$outputHeadSLX.bam";
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my $badsnpsSLX = "$outputBamSLX.badsnps";
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clean($inputBamSLX, $outputBamSLX, $queue, $sting, $dry, $badsnpsSLX);
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call("-I $outputBamSLX", $outputHeadSLX, $queue, $sting, $dry, "$outputBamSLX.cleaner.*", $sample, $badsnpsSLX, $DoC_slx{$sample}, $MQ_hash{"SLX"});
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if ($sample eq "NA12878" || $sample eq "NA19240") {
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my $inputBamSOLID = "$inputDir/$sample.pilot2.SOLID.bam";
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my $outputHeadSOLID = "$outputDir/$sample.SOLID";
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my $outputBamSOLID = "$outputHeadSOLID.bam";
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my $badsnpsSOLID = "$outputBamSOLID.badsnps";
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clean($inputBamSOLID, $outputBamSOLID, $queue, $sting, $dry, $badsnpsSOLID);
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call("-I $outputBamSOLID", $outputHeadSOLID, $queue, $sting, $dry, "$outputBamSOLID.cleaner.*", $sample, $badsnpsSOLID, $DoC_solid{$sample}, $MQ_hash{"SOLID"});
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my $inputBam454 = "$inputDir/$sample.pilot2.454.bam";
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my $outputHead454 = "$outputDir/$sample.454";
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call("-I $inputBam454", $outputHead454, $queue, $sting, $dry, "$outputBamSLX.cleaner.*", $sample, $badsnpsSLX, $DoC_454{$sample}, $MQ_hash{"454"});
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my $outputHead = "$outputDir/$sample.SOLID_454";
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call("-I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "$outputBamSOLID.cleaner.*", $sample, $badsnpsSOLID, $DoC_454solid{$sample}, $MQ_hash{"454SOLID"});
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$outputHead = "$outputDir/$sample.allTechs";
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call("-I $outputBamSLX -I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "*.cleaner.*", $sample, $badsnpsSLX, $DoC_all{$sample}, $MQ_hash{"ALL"});
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}
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}
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sub clean {
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my $inputBam = $_[0];
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my $outputBam = $_[1];
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my $queue = $_[2];
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my $sting = $_[3];
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my $dry = $_[4];
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my $badsnps = $_[5];
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my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -inject -j $outputBam.cleaner.pipeline -sting $sting -badsnps $badsnps";
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if ($dry) {
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$cmd .= " -dry";
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}
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system($cmd);
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}
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sub call {
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my $inputBams = $_[0];
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my $outputHead = $_[1];
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my $queue = $_[2];
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my $sting = $_[3];
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my $dry = $_[4];
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my $wait = $_[5];
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my $sample = $_[6];
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my $badsnps = $_[7];
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my $doc = $_[8];
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my $mq = $_[9];
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my $cmd = "perl $sting/perl/1kgScripts/runCallingPipeline.pl -i \"$inputBams\" -o $outputHead -q $queue -snps -sting $sting -sample $sample -badsnps $badsnps -doc $doc -mq $mq";
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if ($dry) {
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$cmd .= " -dry";
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}
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if ($wait) {
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$cmd .= " -wait $wait";
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}
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system($cmd);
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}
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