Difference between revisions of "GotCloud: Variant Calling Options"
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− | + | === Required Options === | |
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | {| 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 | ! 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|BAM List File]] || $(OUT_DIR)/bam.list |
− | |||
− | |||
|- | |- | ||
| --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) | ||
+ | |} | ||
+ | |||
+ | === Common Options === | ||
+ | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | ||
+ | ! colspan="4" | Common Options | ||
|- | |- | ||
− | + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value | |
− | |||
− | |||
− | |||
− | |||
|- | |- | ||
+ | | --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 | | --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 | ||
|- | |- | ||
Line 23: | Line 28: | ||
format (-end is optional): chr:start-end | format (-end is optional): chr:start-end | ||
| | | | ||
+ | |} | ||
+ | |||
+ | === Cluster 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 | ||
+ | | --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 === | ||
+ | {| 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 | ||
+ | |- | ||
+ | | --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 === | ||
+ | {| 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 | |
|- | |- | ||
− | | -- | + | | --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 || | | --bamprefix ''prefix'' || BAM_PREFIX || path to prepend to relative BAM file paths in the BAM list || | ||
Line 38: | Line 68: | ||
| --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref | | --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 === | ||
+ | {| 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 | ||
|- | |- | ||
− | | -- | + | | --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 || | | --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 === | ||
+ | {| 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 | ||
|- | |- | ||
| --nophonehome || || disable phonehome in GotCloud and the tools it calls || | | --nophonehome || || disable phonehome in GotCloud and the tools it calls || | ||
|- | |- | ||
|} | |} |
Revision as of 11:46, 24 October 2014
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 |