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Revision as of 18:39, 28 January 2016
, 18:39, 28 January 2016→Optional Configurable Settings
=== 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 may specify their own configuration file specifying just the values different than the defaults. The configuration file is not required if there are no values to override.
{{:GotCloud: Configuration}}
==== Recommended Settings ====
As of GotCloud version 1.16, the alignment pipeline uses <code>bwa mem</code> by default. Prior to version 1.16, the default aligner was <code>bwa aln</code>.
You can override the defaults by setting in your configuration file:
* to use <code>bwa mem</code> (you do not need to set this in version 1.16 and later since it is the default)
MAP_TYPE = BWA_MEM
* to use <code>bwa aln</code> (you do not need to set this prior to version 1.16 since it is the default)
MAP_TYPE = BWA
==== Additional Required Settings ====
==== Required Settings ====
See [[#FASTQ List File|FASTQ List File]] for how to set the index file either via command line options or via configuration.
See [[#FASTQ List File|FASTQ List File]] for how to set the index file either via command line options or via configuration.
* BWA_THREADS = -t N
* BWA_THREADS = -t N
** Fill in the N with the number of threads you want BWA to run with, default is 1
** Fill in the N with the number of threads you want BWA to run with, default is 1
* BWA_QUAL = -q N
** Fill in the N with the trim quality you want BWA aln to run with, default is 15. This parameter is only applied to bwa aln. It is not used for BWA_MEM.
* BWA_MEM_OPTS =
** Specify any additional bwa mem options using this parameter.
* SORT_MAX_MEM = 2000000000
* SORT_MAX_MEM = 2000000000
** Maximum amount of memory used by samtools sort after running bwa
** Maximum amount of memory used by samtools sort after running bwa
== Running the Alignment Pipeline ==
== Running the Alignment Pipeline ==
