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diff variant_filtration.xml @ 39:fab099dde911 draft default tip

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VariantFiltration should not have -nt option since it does not implemnt TreeReducible
author Jim Johnson <jj@umn.edu>
date Tue, 05 Mar 2013 11:15:13 -0600
parents 14d47237bb0a
children
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--- a/variant_filtration.xml	Mon Mar 04 21:37:30 2013 -0600
+++ b/variant_filtration.xml	Tue Mar 05 11:15:13 2013 -0600
@@ -12,7 +12,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "VariantFiltration"
     \$GATK2_SITE_OPTIONS
-    \$GATK2_NUM_THREADS
+    ## \$GATK2_NUM_THREADS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     -o "${output_vcf}"