# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1362503713 21600
# Node ID fab099dde911af4aeee49087a40d2d90e0de0520
# Parent  1061731ba6ede4b7c8e684ad2a21fe9b32ee665d
VariantFiltration should not have -nt option since it does not implemnt TreeReducible

diff -r 1061731ba6ed -r fab099dde911 variant_filtration.xml
--- 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}"