97 lines
4.2 KiB
Perl
Executable File
97 lines
4.2 KiB
Perl
Executable File
#!/usr/bin/perl -w
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use strict;
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use FindBin;
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use lib "$FindBin::Bin/../../";
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use StingArgs;
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use DistributedMake;
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use DataTable;
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use Data::Dumper;
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use File::Basename;
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my %args = &getCommandArguments(
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"LIST" => undef,
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"OUT_DIR" => undef,
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"REFERENCE" => "/broad/1KG/reference/human_b36_both.fasta",
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"DBSNP" => "/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod",
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"SEQUENCE_INDEX" => "/broad/1KG/DCC/ftp/sequence.index",
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"ALIGNMENT_INDEX" => "/broad/1KG/DCC/ftp/alignment.index",
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"DRY_RUN" => 1,
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"QUEUE" => "gsa",
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"NUM_JOBS" => "",
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"KEEP_GOING" => 1,
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);
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my $dm = new DistributedMake("dryRun" => $args{'DRY_RUN'}, "queue" => $args{'QUEUE'}, "numJobs" => "", "keepGoing" => 1, "outputFile" => "$args{'OUT_DIR'}/GenerateDataProcessingReport2.log");
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my @entries;
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open(LIST, $args{'LIST'});
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while (my $entry = <LIST>) {
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chomp($entry);
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my %entry;
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($entry{'POP'}, $entry{'UG'}, $entry{'QCALL'}) = split(/\s+/, $entry);
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push(@entries, \%entry);
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}
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close(LIST);
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my @slides;
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foreach my $entry (@entries) {
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my %entry = %{$entry};
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# Combine VCFs
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my $vcfCombineOut = "$args{'OUT_DIR'}/intermediate/$entry{'POP'}.combined.vcf";
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my $vcfCombineOutCmd = "java -Xmx2048m -jar $ENV{'STING_DIR'}/dist/GenomeAnalysisTK.jar -T VCFCombine -R $args{'REFERENCE'} -type UNION -B UG,VCF,$entry{'UG'} -B QCALL,VCF,$entry{'QCALL'} -A -priority 'UG,QCALL' -o $vcfCombineOut -l INFO -L 1";
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$dm->addRule($vcfCombineOut, [$entry{'UG'}, $entry{'QCALL'}], $vcfCombineOutCmd);
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# Evaluate variants
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my $evalRoot = "$vcfCombineOut.eval/eval";
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my $evalCounts = "$evalRoot.Count_Variants.csv";
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my $evalCmd = "java -Xmx2048m -jar $ENV{'STING_DIR'}/dist/GenomeAnalysisTK.jar -T VariantEval -R $args{'REFERENCE'} -D $args{'DBSNP'} -B eval,VCF,$vcfCombineOut -select 'set==\"Intersection\"' -selectName Intersection -select 'set==\"UG-filteredInOther\"' -selectName InUG-FilteredInQCALL -select 'set==\"QCALL-filteredInOther\"' -selectName InQCALL-FilteredInUG -select 'set==\"UG\"' -selectName UG -select 'set==\"QCALL\"' -selectName QCALL -reportType R -reportLocation $evalRoot -l INFO -L 1";
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$dm->addRule($evalCounts, $vcfCombineOut, $evalCmd);
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# Get SNPs per sample
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my $snpsPerSample = "$evalRoot.persample.table";
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my $snpsPerSampleCmd = "$ENV{'STING_DIR'}/perl/reports/1KG/GetSNPsPerSample.pl VCF=$vcfCombineOut OUT=$snpsPerSample";
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$dm->addRule($snpsPerSample, $vcfCombineOut, $snpsPerSampleCmd);
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# Create topsheet slide
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my $slideDir = "$args{'OUT_DIR'}/intermediate/$entry{'POP'}/slides";
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my $topSheetRoot = "$slideDir/$entry{'POP'}.000.topsheet";
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my $topSheetSlide = "$topSheetRoot.pdf";
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my $topSheetSlideCmd = "$ENV{'STING_DIR'}/perl/reports/1KG/MakeTopSheetSlide.pl VCF=$vcfCombineOut SEQUENCE_INDEX=$args{'SEQUENCE_INDEX'} ALIGNMENT_INDEX=$args{'ALIGNMENT_INDEX'} EVAL_ROOT=$evalRoot OUT=$topSheetRoot";
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#$dm->addRule($topSheetSlide, [$vcfCombineOut, $args{'SEQUENCE_INDEX'}, $args{'ALIGNMENT_INDEX'}, $evalCounts], $topSheetSlideCmd);
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# Create Venn diagram slide of variants
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my $vennRoot = "$slideDir/$entry{'POP'}.010.venn";
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my $vennPdf = "$vennRoot.pdf";
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my $vennPdfCmd = "$ENV{'STING_DIR'}/perl/reports/1KG/MakeVennSlide.pl EVAL_ROOT=$evalRoot OUT_ROOT=$vennRoot POP=$entry{'POP'}";
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$dm->addRule($vennPdf, $evalCounts, $vennPdfCmd);
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# Create plots for other slides
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my $plotRoot = "$evalRoot.plot";
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my $plotDummy = "$plotRoot.venn_per_ac.norm.pdf";
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my $plotCmd = "Rscript $ENV{'STING_DIR'}/perl/reports/1KG/MakeDataProcessingReportPlots.R $evalRoot $plotRoot $entry{'POP'}";
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$dm->addRule($plotDummy, [$evalCounts, $snpsPerSample], $plotCmd, 'queue' => "");
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# Create other slides
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my $dprSlideDummy = "$slideDir/$entry{'POP'}.050.eval.plot.titv.pdf";
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my $dprSlidesCmd = "$ENV{'STING_DIR'}/perl/reports/1KG/MakeDPRSlides.pl PLOT_ROOT=$plotRoot OUT_DIR=$slideDir POP=$entry{'POP'}";
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$dm->addRule($dprSlideDummy, $plotDummy, $dprSlidesCmd);
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push(@slides, $dprSlideDummy);
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}
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my $assembledSlides = "$args{'OUT_DIR'}/dpr.pdf";
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my $assembledSlidesCmd = "$ENV{'STING_DIR'}/perl/reports/1KG/AssembleSlides.pl DIR=$args{'OUT_DIR'} OUT=$assembledSlides";
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$dm->addRule($assembledSlides, \@slides, $assembledSlidesCmd);
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$dm->execute();
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