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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 |
|
