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comparison unified_genotyper.xml @ 3:2553f84b8174 draft

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author iuc
date Wed, 19 Feb 2014 04:39:38 -0500
parents 8bcc13094767
children f244b8209eb8
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2:8bcc13094767 3:2553f84b8174
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}"