GotCloud: Variant Calling Options: Difference between revisions
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| --verbose || || Add additional messages when reading configuration || | | --verbose || || Add additional messages when reading configuration || | ||
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===Reference/Resource Files=== | |||
* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings | |||
=== Analysis Region Options === | === Analysis Region Options === | ||
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==== Chromosome X Calling ==== | |||
For proper Chromosome X calling, it is recommended to specify a PED file with sex information: | |||
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | |||
! Configuration Key !! Value Description | |||
|- | |||
|PED_INDEX|| ped file containing sampleID (2nd column) and sex (5th column) | |||
|} | |||
Format of PED file: | |||
:<code>familyID sampleID fatherID motherID sex</code> | |||
* Only <code>sampleID</code> and <code>sex</code> are used | |||
====Targeted/Exome Sequencing Settings==== | |||
If you are running Targeted/Exome Sequencing, the user should specify: | |||
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | |||
! Configuration Key !! Value Description | |||
|- | |||
|UNIFORM_TARGET_BED|| Bed file of targeted regions (same bed for all samples) | |||
|- | |||
|MULTIPLE_TARGET_MAP|| Filename of file mapping: sample id -> bed file of targeted regions | |||
Each line of the file contains: [SM_ID] [TARGET_BED] | |||
|- | |||
|OFFSET_OFF_TARGET|| Number of bases by which to extend the target region | |||
(default is 0, do not extend the target region) | |||
|- | |||
|SAMTOOLS_VIEW_TARGET_ONLY || '''true''': speeds up processing by excluding off-target regions initially when performing samtools view | |||
'''false''' (default): off-target regions are not excluded when performing samtools view, but are excluded at a later step | |||
'''Warning:''' You may not want to set this to true due to it may: | |||
*''make command line too long'' | |||
*''produce an error if reads overlap multiple targeted regions'' | |||
** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]] | |||
|} | |||
=== Path Options === | === Path Options === | ||
Revision as of 12:10, 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 |
Reference/Resource Files
- See GotCloud: Genetic Reference and Resource Files for reference/resource file configuration settings
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 |
Chromosome X Calling
For proper Chromosome X calling, it is recommended to specify a PED file with sex information:
| Configuration Key | Value Description |
|---|---|
| PED_INDEX | ped file containing sampleID (2nd column) and sex (5th column) |
Format of PED file:
familyID sampleID fatherID motherID sex
- Only
sampleIDandsexare used
Targeted/Exome Sequencing Settings
If you are running Targeted/Exome Sequencing, the user should specify:
| Configuration Key | Value Description |
|---|---|
| UNIFORM_TARGET_BED | Bed file of targeted regions (same bed for all samples) |
| MULTIPLE_TARGET_MAP | Filename of file mapping: sample id -> bed file of targeted regions
Each line of the file contains: [SM_ID] [TARGET_BED] |
| OFFSET_OFF_TARGET | Number of bases by which to extend the target region
(default is 0, do not extend the target region) |
| SAMTOOLS_VIEW_TARGET_ONLY | true: speeds up processing by excluding off-target regions initially when performing samtools view
false (default): off-target regions are not excluded when performing samtools view, but are excluded at a later step Warning: You may not want to set this to true due to it may:
|
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 |
