Changes

| --help || || print help information ||  

| --help || || print help information ||  

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| --test || || run the snpcall/ldrefine test ||

| --test ''path'' || || run the snpcall/ldrefine test and write output to the specified path||

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| --conf || || configuration file to use ||

| --conf ''file'' || || configuration file to use ||

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| --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)

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| --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

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| --outdir || OUT_DIR || output directory ||

| --outdir ''path'' || OUT_DIR || output directory ||

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| --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

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| --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

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| --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

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| --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

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| --batchtype || BATCH_TYPE || name of cluster type || local

| --batchtype ''type'' || BATCH_TYPE || name of cluster type || local

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| --batchopts || BATCH_OPTS || options to pass to the cluster command ||  

| --batchopts ''opts'' || BATCH_OPTS || options to pass to the cluster command ||  

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| --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 ||  

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| --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 ||  

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| --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) ||  

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| --refdir || REF_DIR || ||  

| --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref

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|-

| --verbose ||  || Add additional messages when reading configuration

| --verbose ||  || Add additional messages when reading configuration ||

 

2/3: some additional messages & do not die on missing required keys || 0 (no additional messages)

 

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| --copyglf || COPY_GLF ||  ||  

| --copyglf ''path'' || COPY_GLF || path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) ||  

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| --ignoresmcheck || || ||  

| --ignoresmcheck || IGNORE_SM_CHECK || disable the validation that the Sample name in the BAM file matches the one in the BAM list file ||  

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| --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

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| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  

| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  

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