From f8a3bd72433870f601ea5979a6ad3bd1b59b3b45 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 28 Nov 2010 00:45:21 +0000
Subject: [PATCH] A helper script to merge two VCFs, run VariantEval, and the
 VariantReport.R script.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4741 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/MergeAndEvaluateVCFs.pl | 80 ++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100755 perl/MergeAndEvaluateVCFs.pl

diff --git a/perl/MergeAndEvaluateVCFs.pl b/perl/MergeAndEvaluateVCFs.pl
new file mode 100755
index 000000000..e5ad4cf6d
--- /dev/null
+++ b/perl/MergeAndEvaluateVCFs.pl
@@ -0,0 +1,80 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+
+sub getArgs {
+    my %doc = (
+        'GATK'          => "Path to GenomeAnalysisTK.jar (usually in your Sting/dist/ directory)",
+        'VARIANTREPORT' => "Path to VariantReport.R (usually in your Sting/R/VariantReport/ directory)",
+        'REFERENCE'     => "Path to human reference sequence",
+        'DBSNP'         => "Path to dbsnp rod",
+        'VCF1'          => "Path to first VCF file",
+        'VCF1NAME'      => "Name of first VCF file",
+        'VCF2'          => "Path to second VCF file",
+        'VCF2NAME'      => "Name of second VCF file",
+        'VCFOUT'        => "Output root for resultant merged VCF, the eval file, and PDF",
+    );
+
+    my %args = (
+        'GATK'          => undef,
+        'VARIANTREPORT' => undef,
+        'REFERENCE'     => undef,
+        'DBSNP'         => undef,
+        'VCF1'          => undef,
+        'VCF1NAME'      => undef,
+        'VCF2'          => undef,
+        'VCF2NAME'      => undef,
+        'VCFOUT'        => undef,
+    );
+
+    my $result = GetOptions(
+        "GATK=s"          => \$args{'GATK'},
+        "VARIANTREPORT=s" => \$args{'VARIANTREPORT'},
+        "REFERENCE=s"     => \$args{'REFERENCE'},
+        "DBSNP=s"         => \$args{'DBSNP'},
+        "VCF1=s"          => \$args{'VCF1'},
+        "VCF1NAME=s"      => \$args{'VCF1NAME'},
+        "VCF2=s"          => \$args{'VCF2'},
+        "VCF2NAME=s"      => \$args{'VCF2NAME'},
+        "VCFOUT=s"        => \$args{'VCFOUT'},
+    );
+
+    my @undefinedArgs;
+    foreach my $key (sort { $a cmp $b } keys(%args)) {
+        if (!defined($args{$key})) {
+            push(@undefinedArgs, $key);
+        }
+    }
+
+    if (scalar(@undefinedArgs) > 0) {
+        print "Error: there were some undefined arguments:\n";
+
+        foreach my $undefinedArg (@undefinedArgs) {
+            print "\t-$undefinedArg : $doc{$undefinedArg}\n";
+        }
+
+        exit(-1);
+    }
+
+    return %args;
+}
+
+sub runCommand {
+    my ($output, $cmd) = @_;
+
+    #if (!-e $output) {
+        system($cmd);
+    #}
+}
+
+my %args = &getArgs();
+
+my $combineVariantsCmd = "java -jar $args{'GATK'} -T CombineVariants -R $args{'REFERENCE'} -B:$args{'VCF1NAME'},VCF $args{'VCF1'} -B:$args{'VCF2NAME'},VCF $args{'VCF2'} -variantMergeOptions UNION -priority $args{'VCF1NAME'},$args{'VCF2NAME'} -o $args{'VCFOUT'} -l INFO";
+&runCommand($args{'VCFOUT'}, $combineVariantsCmd);
+
+my $variantEvalCmd = "java -jar $args{'GATK'} -T VariantEval -R $args{'REFERENCE'} -D $args{'DBSNP'} -B:eval,VCF $args{'VCFOUT'} -select 'set==\"Intersection\"' -selectName Intersection -select 'set==\"$args{'VCF1NAME'}\"' -selectName $args{'VCF1NAME'} -select 'set==\"filterIn$args{'VCF1NAME'}-$args{'VCF2NAME'}\"' -selectName In$args{'VCF2NAME'}-FilteredIn$args{'VCF1NAME'} -select 'set==\"$args{'VCF2NAME'}\"' -selectName $args{'VCF2NAME'} -select 'set==\"filterIn$args{'VCF2NAME'}-$args{'VCF1NAME'}\"' -selectName In$args{'VCF1NAME'}-FilteredIn$args{'VCF2NAME'} -select 'set==\"FilteredInAll\"' -selectName FilteredInAll -reportType R -reportLocation $args{'VCFOUT'}.eval";
+&runCommand("$args{'VCFOUT'}.eval", $variantEvalCmd);
+
+my $variantReportCmd = "Rscript $args{'VARIANTREPORT'} -title 'Automated Variant Report' -author '$ENV{'USER'}' -evalRoot $args{'VCFOUT'}.eval -plotOut $args{'VCFOUT'}.eval.pdf";
+&runCommand("$args{'VCFOUT'}.eval.pdf", $variantReportCmd);