Mercurial > repos > iuc > gatk2
comparison unified_genotyper.xml @ 3:2553f84b8174 draft
Uploaded
author | iuc |
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date | Wed, 19 Feb 2014 04:39:38 -0500 |
parents | 8bcc13094767 |
children | f244b8209eb8 |
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2:8bcc13094767 | 3:2553f84b8174 |
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20 --out "${output_vcf}" | 20 --out "${output_vcf}" |
21 --metrics_file "${output_metrics}" | 21 --metrics_file "${output_metrics}" |
22 \$GATK2_SITE_OPTIONS | 22 \$GATK2_SITE_OPTIONS |
23 | 23 |
24 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 | 24 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 |
25 --num_cpu_threads_per_data_thread 6 | 25 --num_cpu_threads_per_data_thread 1 |
26 | 26 |
27 #if $reference_source.reference_source_selector != "history": | 27 #if $reference_source.reference_source_selector != "history": |
28 -R "${reference_source.ref_file.fields.path}" | 28 -R "${reference_source.ref_file.fields.path}" |
29 #end if | 29 #end if |
30 --genotype_likelihoods_model "${genotype_likelihoods_model}" | 30 --genotype_likelihoods_model "${genotype_likelihoods_model}" |