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comparison 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
comparison
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38:1061731ba6ed 39:fab099dde911
10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" 10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
11 -p 'java 11 -p 'java
12 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 12 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
13 -T "VariantFiltration" 13 -T "VariantFiltration"
14 \$GATK2_SITE_OPTIONS 14 \$GATK2_SITE_OPTIONS
15 \$GATK2_NUM_THREADS 15 ## \$GATK2_NUM_THREADS
16 ##--num_threads 4 ##hard coded, for now 16 ##--num_threads 4 ##hard coded, for now
17 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home 17 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
18 -o "${output_vcf}" 18 -o "${output_vcf}"
19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
20 #if $reference_source.reference_source_selector != "history": 20 #if $reference_source.reference_source_selector != "history":