Difference between revisions of "GotCloud: Variant Calling Options"

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

Revision as of 12:10, 24 October 2014

Required Options

Command-line Flag Configuration Key Value Description Default Value
--outdir path OUT_DIR output directory
--list/--bam_list/--bamlist file BAM_LIST path to the BAM List File $(OUT_DIR)/bam.list
--numjobs # number of jobs to run in parallel 0 (generate Makefile of steps, but do not run)

Common Options

Common Options
Command-line Flag Configuration Key Value Description Default Value
--conf file configuration file to use

Cluster Options

Command-line Flag Configuration Key Value Description Default Value
--batchtype type BATCH_TYPE name of cluster type local
--batchopts opts BATCH_OPTS options to pass to the cluster command
--copyglf path COPY_GLF path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp)

Test/Debug Options

Command-line Flag Configuration Key Value Description Default Value
--help print help information
--test path run the snpcall/ldrefine test and write output to the specified path
--verbose Add additional messages when reading configuration

Reference/Resource Files

Analysis Region Options

Command-line Flag Configuration Key Value Description Default Value
--chrs # # CHRS pace separated list of chromosomes to process 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
--region #:#-# call region - skip regions of chromosome outside of specified region

format (-end is optional): chr:start-end

Chromosome X Calling

For proper Chromosome X calling, it is recommended to specify a PED file with sex information:

Configuration Key Value Description
PED_INDEX ped file containing sampleID (2nd column) and sex (5th column)

Format of PED file:

familyID sampleID fatherID motherID sex
  • Only sampleID and sex are used

Targeted/Exome Sequencing Settings

If you are running Targeted/Exome Sequencing, the user should specify:

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 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:


Path Options

Command-line Flag Configuration Key Value Description Default Value
--makebasename name MAKE_BASE_NAME basename of the Makefile generated by GotCloud umake
--bamprefix prefix BAM_PREFIX path to prepend to relative BAM file paths in the BAM list
--refprefix prefix REF_PREFIX path to prepend to relative reference/resource file paths
--baseprefix prefix BASE_PREFIX path to prepend to relative paths for the BAM list file, PED_INDEX, BAM (if BAM_PREFIX isn't specified), reference/resource files (if REF_PREFIX isn't specified)
--refdir path REF_DIR value to use for REF_DIR key $(GOTCLOUD_ROOT)/gotcloud.ref
--gotcloudroot path GOTCLOUD_ROOT specify to use a different directory for finding GotCloud bins/scripts based on the location of the gotcloud/umake.pl script

Validation Adjustment Options

Command-line Flag Configuration Key Value Description Default Value
--maxlocaljobs # maximum # of jobs that can run if batchtype is local (to prevent accidentally starting jobs locally that were meant to be on a cluster) 10
--ignoresmcheck IGNORE_SM_CHECK disable the validation that the Sample name in the BAM file matches the one in the BAM list file

Miscellaneous Options

Command-line Flag Configuration Key Value Description Default Value
--nophonehome disable phonehome in GotCloud and the tools it calls
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