68 lines
2.3 KiB
Perl
68 lines
2.3 KiB
Perl
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#!/usr/bin/perl -w
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use strict;
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use Getopt::Long;
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my $pilot = "pilot2";
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my $queue = "gsa";
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my $tech = "SLX";
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my $jar = "/humgen/gsa-scr1/ebanks/Sting/dist/GenomeAnalysisTK.jar";
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GetOptions( "p:s" => \$pilot,
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"q:s" => \$queue,
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"tech:s" => \$tech,
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"j:s" => \$jar );
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my @samples;
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if ($pilot eq "pilot1") {
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@samples = ("CEU","YRI","CHB-JPT");
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} elsif ($pilot eq "pilot2") {
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@samples = ("NA19238","NA19239","NA19240","NA12878","NA12891","NA12892");
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}
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foreach my $sample (@samples) {
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enqueue($sample, $pilot, $queue, $jar, $tech);
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}
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sub enqueue {
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my $sample = $_[0];
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my $pilot = $_[1];
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my $queue = $_[2];
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my $jar = $_[3];
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my $tech = $_[4];
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my $inputBamStr = "";
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my $outputDir;
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if ($pilot eq "pilot2") {
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$inputBamStr = "-I /humgen/gsa-hphome1/projects/1kg_pilot2/useTheseBamsForAnalyses/$sample.$tech.bam";
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$outputDir = "/broad/hptmp/ebanks/1kg_pilot2/cleaned/calls";
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} else {
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my $num = 1;
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while ($num < 23) {
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$inputBamStr .= "-I /broad/hptmp/ebanks/1kg_pilot1/cleaned/bams/$sample.chr$num.$tech.bam ";
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$num++;
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}
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$inputBamStr .= "-I /broad/hptmp/ebanks/1kg_pilot1/cleaned/bams/$sample.chrX.$tech.bam -I /broad/hptmp/ebanks/1kg_pilot1/cleaned/bams/$sample.chrY.$tech.bam ";
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$outputDir = "/broad/hptmp/ebanks/1kg_pilot1/cleaned/calls";
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}
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my $outputFile = "$outputDir/indels/$sample.$tech.low.calls";
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my $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -o $outputFile -minConsensusFraction 0.5 -minFraction 0.";
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if ($pilot eq "pilot1") { $cmd .= "0"; }
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$cmd .= "1 -minCnt 2 -1kg";
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system($cmd);
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$outputFile = "$outputDir/indels/$sample.$tech.high.calls";
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -o $outputFile -minConsensusFraction 0.5 -minFraction 0.";
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if ($pilot eq "pilot1") { $cmd .= "0"; }
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$cmd .= "3 -minCnt 2 -1kg";
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system($cmd);
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if ($pilot eq "pilot2") {
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$outputFile = "$outputDir/unfiltered_snps/$sample.$tech.geli.calls";
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T SingleSampleGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $outputFile -lod 5";
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system($cmd);
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}
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}
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