GotCloud: Variant Calling Options: Difference between revisions
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| --help || || print help information || | | --help || || print help information || | ||
|- | |- | ||
| --test || || run the snpcall/ldrefine test || | | --test ''path'' || || run the snpcall/ldrefine test and write output to the specified path|| | ||
|- | |- | ||
| --conf || || configuration file to use || | | --conf ''file'' || || configuration file to use || | ||
|- | |- | ||
| --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) | ||
|- | |- | ||
| --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 | | --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 || | | --outdir ''path'' || OUT_DIR || output directory || | ||
|- | |- | ||
| --list/--bam_list/--bamlist || BAM_LIST || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list | | --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM List File|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 | | --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 | | --region ''#:#-#'' || || call region - skip regions of chromosome outside of specified region | ||
format (-end is optional): chr:start-end | format (-end is optional): chr:start-end | ||
| | | | ||
|- | |- | ||
| --makebasename || MAKE_BASE_NAME || basename of the Makefile generated by GotCloud || umake | | --makebasename ''name'' || MAKE_BASE_NAME || basename of the Makefile generated by GotCloud || umake | ||
|- | |- | ||
| --batchtype || BATCH_TYPE || name of cluster type || local | | --batchtype ''type'' || BATCH_TYPE || name of cluster type || local | ||
|- | |- | ||
| --batchopts || BATCH_OPTS || options to pass to the cluster command || | | --batchopts ''opts'' || BATCH_OPTS || options to pass to the cluster command || | ||
|- | |- | ||
| --bamprefix || 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 || | ||
|- | |- | ||
| --refprefix || REF_PREFIX || path to prepend to relative reference/resource file paths || | | --refprefix ''prefix'' || 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) || | | --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 || REF_DIR || | | --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref | ||
|- | |- | ||
| --verbose || || Add additional messages when reading configuration | | --verbose || || Add additional messages when reading configuration || | ||
|- | |- | ||
| --copyglf || COPY_GLF || || | | --copyglf ''path'' || COPY_GLF || path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) || | ||
|- | |- | ||
| --ignoresmcheck || | | --ignoresmcheck || IGNORE_SM_CHECK || disable the validation that the Sample name in the BAM file matches the one in the BAM list file || | ||
|- | |- | ||
| --gotcloudroot || GOTCLOUD_ROOT || specify to use a different directory for finding GotCloud bins/scripts || based on the location of the gotcloud/umake.pl script | | --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 | ||
|- | |- | ||
| --nophonehome || || disable phonehome in GotCloud and the tools it calls || | | --nophonehome || || disable phonehome in GotCloud and the tools it calls || | ||
|- | |- | ||
|} | |} | ||
Revision as of 11:32, 24 October 2014
| 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 | ||
| --conf file | 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 path | OUT_DIR | output directory | |
| --list/--bam_list/--bamlist file | 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 name | MAKE_BASE_NAME | basename of the Makefile generated by GotCloud | umake |
| --batchtype type | BATCH_TYPE | name of cluster type | local |
| --batchopts opts | BATCH_OPTS | options to pass to the cluster command | |
| --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 |
| --verbose | Add additional messages when reading configuration | ||
| --copyglf path | COPY_GLF | path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) | |
| --ignoresmcheck | IGNORE_SM_CHECK | disable the validation that the Sample name in the BAM file matches the one in the BAM list file | |
| --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 |
| --nophonehome | disable phonehome in GotCloud and the tools it calls |
