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GotCloud: Variant Calling Pipeline (view source)

Revision as of 18:14, 23 October 2014

280 bytes added ,  18:14, 23 October 2014
→‎Configuration File
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====Additional Required User Config Files Settings====
 
====Additional Required User Config Files Settings====
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The following Config File Settings must be specified by the user:
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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* CHRS = space separated list of chromosomes you want
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! Configuration Key !! Command-line Flag !! Value Description !! Default Value
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* BAM_INDEX = path to the Index File of BAMs
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|-
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|CHRS||--chrs || pace separated list of chromosomes to process || 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
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|-
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| BAM_LIST|| --list || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list
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|}
    
====Targeted/Exome Sequencing Settings====
 
====Targeted/Exome Sequencing Settings====
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11871"

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