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Revision as of 18:01, 23 October 2014
, 18:01, 23 October 2014→Configuration File
== Configuration File ==
== Configuration File ==
Configuration file contains the run-time options including the software binaries and command line arguments. A default configuration file is automatically loaded. Users must specify their own configuration file specifying just the values different than the defaults.
{{:GotCloud: Configuration}}
===Additional Required User Config Files Settings===
===Required User Config Files Settings===
The following Config File Settings must be specified by the user:
The following Config File Settings must be specified by the user:
* CHRS = space separated list of chromosomes you want
* CHRS = space separated list of chromosomes you want
* BAM_INDEX = path to the Index File of BAMs
* BAM_INDEX = path to the Index File of BAMs
===Targeted/Exome Sequencing Settings===
===Targeted/Exome Sequencing Settings===
* Extend the target region by a given number of bases, for example: 50
* Extend the target region by a given number of bases, for example: 50
** OFFSET_OFF_TARGET = 50
** OFFSET_OFF_TARGET = 50
=== Chromosome X Calling ===
=== Chromosome X Calling ===
