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comparison indel_realigner.xml @ 2:8bcc13094767 draft

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author iuc
date Sat, 18 Jan 2014 07:21:33 -0500
parents 340633249b3d
children f244b8209eb8
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1:f760c0de8e3a 2:8bcc13094767
18 18
19 \$GATK2_SITE_OPTIONS 19 \$GATK2_SITE_OPTIONS
20 20
21 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 21 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
22 --num_cpu_threads_per_data_thread 1 22 --num_cpu_threads_per_data_thread 1
23
24 @THREADS@
25 23
26 #if $reference_source.reference_source_selector != "history": 24 #if $reference_source.reference_source_selector != "history":
27 -R "${reference_source.ref_file.fields.path}" 25 -R "${reference_source.ref_file.fields.path}"
28 #end if 26 #end if
29 -LOD "${lod_threshold}" 27 -LOD "${lod_threshold}"