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Revision as of 14:32, 6 November 2012
, 14:32, 6 November 2012no edit summary
FASTQs can be converted to this type of BAM using the [[Mapping Pipeline]].
FASTQs can be converted to this type of BAM using the [[Mapping Pipeline]].
=== Index File ===
=== Index File ===
Each line of the index file represents each individual under the following format. Note that multiple BAMs per individual may be provided.
Each line of the index file represents each individual under the following format. Note that multiple BAMs per individual may be provided.
=== Configuration File ===
=== Configuration File ===
A default configuration file is automatically loaded. Users must specify their own configuration file specifying just the values different than the defaults.
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.
Comments begin with a <code>#</code>
Comments begin with a <code>#</code>
Where KEY is the item being set and value is its new value
Where KEY is the item being set and value is its new value
====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
====Required on Command-Line or in Config File====
====Required on Command-Line or in Config File====
The following Command-Line or Config File Settings must be specified by the user:
The following Command-Line or Config File Settings must be specified by the user:
* --outdir/OUTDIR= # path to desired output directory
* --outdir/OUTDIR= path to desired output directory
====Targeted/Exome Sequencing Settings====
====Targeted/Exome Sequencing Settings====
* Exclude off-target regions when using samtools view (may make command line too long)
* Exclude off-target regions when using samtools view (may make command line too long)
** SAMTOOLS_VIEW_TARGET_ONLY = TRUE
** SAMTOOLS_VIEW_TARGET_ONLY = TRUE
==== Configure Reference Files ====
==== Configure Reference Files ====
<code>
<code>
'''/usr/local/biopipe/bin/umake.pl --conf umake.conf --snpcall --numjobs 2
'''/usr/local/biopipe/bin/umake --conf myconf ???'''
</code>
</code>
Replace umake.conf with the approprate path/name of the user's configuration file.
If <code>OUTDIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.
Update the value following <code>--numjobs</code> to the appropriate number of jobs that the user wants to run in parallel.
== Running on a Cluster ==
To run on the Cluster, the following settings need to be added to the configuration file:
SLEEP_MULT = 20
MOS_PREFIX = # PREFIX FOR MOSIX COMMAND (BLANK IF UNUSED)
MOS_NODES = # COMMA-SEPARATED LIST OF NODES TO SUBMIT JOBS
REMOTE_PREFIX = # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir])
Set the MOS_NODES to the appropriate node list.
Update MOS_PREFIX to the applicable prefix.
* For MOSIX, use:
MOS_PREFIX = mosrun -E/tmp -t -i
