GotCloud: Variant Calling Options

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

• See GotCloud: Genetic Reference and Resource Files for reference/resource file configuration settings

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: make command line too long produce an error if reads overlap multiple targeted regions see: GotCloud: FAQs->Targetted/Exome

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