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| '''Replace the specified paths to the path to these files.''' | | '''Replace the specified paths to the path to these files.''' |
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| + | ==GotCloud/GenomeSTRiP Command-line Options/Configuration Settings== |
| + | |
| + | === Required 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 |
| + | |- |
| + | | --outdir ''path'' || OUT_DIR || output directory || |
| + | |- |
| + | | --list ''file'' || BAM_LIST || path to the [[GotCloud: Variant Calling Pipeline#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) |
| + | |} |
| + | |
| + | === 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 || |
| + | |} |
| + | |
| + | === 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 |
| + | |- |
| + | | --mosix-opt ''opts'' || GENOMESTRIP_MOSIX_OPT || options to pass to the mosix command || |
| + | |- |
| + | |} |
| + | |
| + | === 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 |
| + | |- |
| + | | --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 === |
| + | See [[#Targeted/Exome Sequencing Settings|Targeted/Exome Sequencing Settings]] for more information on specifying exome/targetted regions and other settings. |
| + | |
| + | {| 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 ''#:#-#'' || GENOMESTRIP_REGION || call region - skip regions of chromosome outside of specified region |
| + | format (-end is optional): chr:start-end |
| + | | |
| + | |- |
| + | |} |
| + | |
| + | === 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 |
| + | |- |
| + | | --bam-prefix ''prefix'' || BAM_PREFIX || path to prepend to relative BAM file paths in the BAM list || |
| + | |- |
| + | | --ref-prefix ''prefix'' || REF_PREFIX || path to prepend to relative reference/resource file paths || |
| + | |- |
| + | | --base-prefix ''prefix'' || BASE_PREFIX || path to prepend to relative paths for the BAM list file, BAM (if BAM_PREFIX isn't specified), reference/resource files (if REF_PREFIX isn't specified) || |
| + | |- |
| + | | --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 |
| + | |- |
| + | |} |
| + | |
| | | |
| == Running GotCloud/GenomeSTRiP == | | == Running GotCloud/GenomeSTRiP == |