From e9eeed8c6f7d093e2cce86ff9fae4bab9e9210f0 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 22 Sep 2009 01:41:58 +0000
Subject: [PATCH] add wait id for 454

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1678 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/1kgScripts/runPilot2Pipeline.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/perl/1kgScripts/runPilot2Pipeline.pl b/perl/1kgScripts/runPilot2Pipeline.pl
index 91245ca8c..58c634859 100755
--- a/perl/1kgScripts/runPilot2Pipeline.pl
+++ b/perl/1kgScripts/runPilot2Pipeline.pl
@@ -58,7 +58,7 @@ foreach my $sample (@samples) {
 
 	my $inputBam454 = "$inputDir/$sample.pilot2.454.bam";
 	my $outputHead454 = "$outputDir/$sample.454";
-	call("-I $inputBam454", $outputHead454, $queue, $sting, $dry, undef, $sample, $badsnpsSLX, $DoC_454{$sample}, $MQ_hash{"454"});
+	call("-I $inputBam454", $outputHead454, $queue, $sting, $dry, "$outputBamSLX.cleaner.*", $sample, $badsnpsSLX, $DoC_454{$sample}, $MQ_hash{"454"});
 
 	my $outputHead = "$outputDir/$sample.SOLID_454";
 	call("-I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "$outputBamSOLID.cleaner.*", $sample, $badsnpsSOLID, $DoC_454solid{$sample}, $MQ_hash{"454SOLID"});