Difference between revisions of "GotCloud: Variant Calling Options"
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| --conf ''file'' || || configuration file to use || | | --conf ''file'' || || configuration file to use || | ||
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| --verbose || || Add additional messages when reading configuration || | | --verbose || || Add additional messages when reading configuration || | ||
+ | |} | ||
+ | |||
+ | === 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 | ||
+ | |- | ||
+ | | --region ''#:#-#'' || || call region - skip regions of chromosome outside of specified region | ||
+ | format (-end is optional): chr:start-end | ||
+ | | | ||
|} | |} | ||
Revision as of 11:54, 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 |
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 |
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 |
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 |