Difference between revisions of "GotCloud: Variant Calling Options"

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(Created page with " {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" ! Command-line Flag !! Configura...")
 
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| --help || || print help information ||  
 
| --help || || print help information ||  
 
|-
 
|-
−
| --test || || run the snpcall/ldrefine test ||
+
| --test ''path'' || || run the snpcall/ldrefine test and write output to the specified path||
 
|-
 
|-
−
| --conf || || configuration file to use ||
+
| --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)
 
|-
 
|-
−
| --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
+
| --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
 
|-
 
|-
−
| --outdir || OUT_DIR || output directory ||
+
| --outdir ''path'' || OUT_DIR || output directory ||
 
|-
 
|-
−
| --list/--bam_list/--bamlist || BAM_LIST || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list
+
| --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list
 
|-
 
|-
−
| --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
 
|-
 
|-
−
| --region || || call region - skip regions of chromosome outside of specified region
+
| --region ''#:#-#'' || || call region - skip regions of chromosome outside of specified region
 
format (-end is optional): chr:start-end
 
format (-end is optional): chr:start-end
 
|  
 
|  
 
|-
 
|-
−
| --makebasename || MAKE_BASE_NAME || basename of the Makefile generated by GotCloud || umake
+
| --makebasename ''name'' || MAKE_BASE_NAME || basename of the Makefile generated by GotCloud || umake
 
|-
 
|-
−
| --batchtype || BATCH_TYPE || name of cluster type || local
+
| --batchtype ''type'' || BATCH_TYPE || name of cluster type || local
 
|-
 
|-
−
| --batchopts || BATCH_OPTS || options to pass to the cluster command ||  
+
| --batchopts ''opts'' || BATCH_OPTS || options to pass to the cluster command ||  
 
|-
 
|-
−
| --bamprefix || 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 ||  
 
|-
 
|-
−
| --refprefix || REF_PREFIX || path to prepend to relative reference/resource file paths ||  
+
| --refprefix ''prefix'' || REF_PREFIX || path to prepend to relative reference/resource file paths ||  
 
|-
 
|-
−
| --baseprefix || 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) ||  
+
| --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 || REF_DIR || ||  
+
| --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref
 
|-
 
|-
−
| --verbose ||  || Add additional messages when reading configuration
+
| --verbose ||  || Add additional messages when reading configuration ||
−
1: some additional messages
 
−
 
 
−
2/3: some additional messages & do not die on missing required keys || 0 (no additional messages)
 
−
 
 
−
4: maximum amount of additional messages & do not die on missing required keys
 
−
| 0 (no additional messages)
 
 
|-
 
|-
−
| --copyglf || COPY_GLF ||  ||  
+
| --copyglf ''path'' || COPY_GLF || path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) ||  
 
|-
 
|-
−
| --ignoresmcheck || || ||  
+
| --ignoresmcheck || IGNORE_SM_CHECK || disable the validation that the Sample name in the BAM file matches the one in the BAM list file ||  
 
|-
 
|-
−
| --gotcloudroot || GOTCLOUD_ROOT || specify to use a different directory for finding GotCloud bins/scripts || based on the location of the gotcloud/umake.pl script
+
| --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
 
|-
 
|-
 
| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  
 
| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  
 
|-
 
|-
 
|}
 
|}

Revision as of 11:32, 24 October 2014


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
--conf file configuration file to use
--numjobs # number of jobs to run in parallel 0 (generate Makefile of steps, but do not run)
--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
--outdir path OUT_DIR output directory
--list/--bam_list/--bamlist file BAM_LIST path to the BAM List File $(OUT_DIR)/bam.list
--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

--makebasename name MAKE_BASE_NAME basename of the Makefile generated by GotCloud umake
--batchtype type BATCH_TYPE name of cluster type local
--batchopts opts BATCH_OPTS options to pass to the cluster command
--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
--verbose Add additional messages when reading configuration
--copyglf path COPY_GLF path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp)
--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
--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=11881"