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Revision as of 12:10, 24 October 2014
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| --verbose || || Add additional messages when reading configuration ||
| --verbose || || Add additional messages when reading configuration ||
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===Reference/Resource Files===
* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings
=== Analysis Region Options ===
=== Analysis Region Options ===
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==== Chromosome X Calling ====
For proper Chromosome X calling, it is recommended to specify a PED file with sex information:
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Value Description
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|PED_INDEX|| ped file containing sampleID (2nd column) and sex (5th column)
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Format of PED file:
:<code>familyID sampleID fatherID motherID sex</code>
* Only <code>sampleID</code> and <code>sex</code> are used
====Targeted/Exome Sequencing Settings====
If you are running Targeted/Exome Sequencing, the user should specify:
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Value Description
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|UNIFORM_TARGET_BED|| Bed file of targeted regions (same bed for all samples)
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|MULTIPLE_TARGET_MAP|| Filename of file mapping: sample id -> bed file of targeted regions
Each line of the file contains: [SM_ID] [TARGET_BED]
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|OFFSET_OFF_TARGET|| Number of bases by which to extend the target region
(default is 0, do not extend the target region)
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|SAMTOOLS_VIEW_TARGET_ONLY || '''true''': speeds up processing by excluding off-target regions initially when performing samtools view
'''false''' (default): off-target regions are not excluded when performing samtools view, but are excluded at a later step
'''Warning:''' You may not want to set this to true due to it may:
*''make command line too long''
*''produce an error if reads overlap multiple targeted regions''
** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]]
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=== Path Options ===
=== Path Options ===
