73 lines
1.8 KiB
Perl
Executable File
73 lines
1.8 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 runPilot1Pipeline.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 $sting = "/humgen/gsa-scr1/ebanks/Sting";
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GetOptions( "i=s" => \$inputDir,
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"odir=s" => \$outputDir,
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"q:s" => \$queue,
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"dry!" => \$dry,
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"sting:s" => \$sting );
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usage() if ( !$inputDir || !$outputDir );
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my @samples = ("ceu","yri","chb_jpt");
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foreach my $sample (@samples) {
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my $inputBam = "$inputDir/low_coverage_$sample.bam";
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my $outputHead = "$outputDir/$sample";
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my $outputBam = "$outputHead.bam";
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my $badsnps = "$outputBam.badsnps";
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clean($inputBam, $outputBam, $queue, $sting, $dry, $badsnps);
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call("-I $outputBam", $outputHead, $queue, $sting, $dry, "$inputBam.cleaner.*", $sample, $badsnps);
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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 -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 $cmd = "perl $sting/perl/1kgScripts/runCallingPipeline.pl -i $inputBams -o $outputHead -q $queue -sting $sting -frac 0 -sample $sample -badsnps $badsnps";
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if ($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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