Difference between revisions of "GotCloud: Variant Calling Options"

Revision as of 11:54, 24 October 2014

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

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)

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

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

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

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

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

@@ Line 18: / Line 18: @@
 |-
 | --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
-|-
-| --region ''#:#-#'' || || call region - skip regions of chromosome outside of specified region
-format (-end is optional): chr:start-end
-|
 |}
@@ Line 53: / Line 42: @@
 |-
 | --verbose ||  || Add additional messages when reading configuration ||
+|}
+=== 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
+|-
+| --region ''#:#-#'' || || call region - skip regions of chromosome outside of specified region
+format (-end is optional): chr:start-end
+|
 |}