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Revision as of 18:30, 23 October 2014
, 18:30, 23 October 2014→Targeted/Exome Sequencing Settings
====Targeted/Exome Sequencing Settings====
====Targeted/Exome Sequencing Settings====
If you are running Targeted/Exome Sequencing, the user should specify:
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
|-
|UNIFORM_TARGET_BED|| Bed file of targeted regions (same bed for all samples)
|-
|MULTIPLE_TARGET_MAP|| Filename of file mapping: sample id -> bed file of targeted regions
Each line of the file contains: [SM_ID] [TARGET_BED]
|-
|OFFSET_OFF_TARGET|| Number of bases by which to extend the target region
(default is 0, do not extend the target region)
|-
|SAMTOOLS_VIEW_TARGET_ONLY || When performing samtools view, if set to true, exclude off-target regions
(default is false)
You may not want to set this to true due to it may:
* Specify the file containing the sample id -> bed map, for example: targetMap.txt
*''make command line too long''
** MULTIPLE_TARGET_MAP = targetMap.txt
*''produce an error if reads overlap multiple targeted regions''
*** Each line of the file contains [SM_ID] [TARGET_BED]
** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]]
|}
==== Chromosome X Calling ====
==== Chromosome X Calling ====
