GotCloud: Variant Calling Options: Difference between revisions

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=== Required Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
|-
| --help || || print help information ||  
| --outdir ''path'' || OUT_DIR || output directory ||
|-
|-
| --test ''path'' || || run the snpcall/ldrefine test and write output to the specified path||
| --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list
|-
| --conf ''file'' || || configuration file to use ||
|-
|-
| --numjobs ''#'' || || number of jobs to run in parallel || 0 (generate Makefile of steps, but do not run)
| --numjobs ''#'' || || number of jobs to run in parallel || 0 (generate Makefile of steps, but do not run)
|}
=== Common Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! colspan="4" | Common Options
|-
|-
| --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
! 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|BAM List File]] || $(OUT_DIR)/bam.list
|-
|-
| --conf ''file'' || || configuration file to use ||
|}
=== Analysis Region Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! 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
| --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
|-
|-
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format (-end is optional): chr:start-end
format (-end is optional): chr:start-end
|  
|  
|}
=== Cluster Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! 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 ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-
! 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||
|-
|-
| --makebasename ''name'' || MAKE_BASE_NAME || basename of the Makefile generated by GotCloud || umake
| --verbose || || Add additional messages when reading configuration ||
|}
 
=== Path Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-
|-
| --batchtype ''type'' || BATCH_TYPE || name of cluster type || local
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
|-
| --batchopts ''opts'' || BATCH_OPTS || options to pass to the cluster command ||  
| --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 ||  
| --bamprefix ''prefix'' || BAM_PREFIX || path to prepend to relative BAM file paths in the BAM list ||  
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| --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref
| --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref
|-
|-
| --verbose || || Add additional messages when reading configuration ||
| --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 ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
|-
| --copyglf ''path'' || COPY_GLF || path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) ||  
| --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 ||  
| --ignoresmcheck || IGNORE_SM_CHECK || disable the validation that the Sample name in the BAM file matches the one in the BAM list file ||  
|-
|-
| --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
|}
 
=== Miscellaneous Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
|-
| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  
| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  
|-
|-
|}
|}

Revision as of 11:46, 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

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

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

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
Retrieved from "http://genome.sph.umich.edu/w/index.php?title=GotCloud:_Variant_Calling_Options&oldid=11882"