GotCloud: Variant Calling Options

Command-line Flag	Configuration Key	Value Description	Default Value
--help		print help information
--test		run the snpcall/ldrefine test
--conf		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	OUT_DIR	output directory
--list/--bam_list/--bamlist	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	MAKE_BASE_NAME	basename of the Makefile generated by GotCloud	umake
--batchtype	BATCH_TYPE	name of cluster type	local
--batchopts	BATCH_OPTS	options to pass to the cluster command
--bamprefix	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
--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)
--refdir	REF_DIR
--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
--ignoresmcheck
--gotcloudroot	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