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SSG -> UG 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1790 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-08 17:40:09 +00:00
parent 008455915a
commit b39a307a04
1 changed files with 2 additions and 2 deletions
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4
perl/1kgScripts/runCallingPipeline.pl
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@ -58,7 +58,7 @@ if ($snps) {
if ($wait) {
$bsub .= " -w \"ended($wait)\"";
}
$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T SingleSampleGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $snpsFile -lod 5.0";
$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $snpsFile -lod 0.0";
execute("$bsub $command", $dry);
my $filterFile = "$outputHead.snps.filtered.calls";
@ -68,7 +68,7 @@ if ($snps) {
if ($badsnps) {
$command .= "cleaned,CleanedOutSNP,$badsnps,";
}
$command .= "indels,SimpleIndel,$indelsLow -X DepthOfCoverage:max=$doc -X AlleleBalance:low=0.25,high=0.75 -X FisherStrand:pvalue=0.00001 -X LodThreshold:lod=5 -X MappingQualityZero:max=$mq -X IndelArtifact -X ClusteredSnps:window=7,snps=3";
$command .= "indels,SimpleIndel,$indelsLow -X DepthOfCoverage:max=$doc -X AlleleBalance:low=0.25,high=0.75 -X FisherStrand:pvalue=0.00001 -X LodThreshold:lod=5.0 -X MappingQualityZero:max=$mq -X IndelArtifact -X ClusteredSnps:window=7,snps=3";
execute("$bsub $command", $dry);
}