Mercurial > repos > jjohnson > gatk2
comparison variant_filtration.xml @ 28:6ef8eb568700 draft
Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 18 Feb 2013 15:48:46 -0600 |
| parents | 7533db8dfb5b |
| children | 76f8ca47b810 |
comparison
equal
deleted
inserted
replaced
| 27:b23ecdd665d0 | 28:6ef8eb568700 |
|---|---|
| 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_THREAD_OPTIONS | 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": |