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Revision as of 21:37, 18 March 2015
, 21:37, 18 March 2015→Example Command Line
====Inputs====
====Inputs====
* Single merged, recalibrated, and deduped BAM file for each subject (stored in a [[#BAM_LIST File for bamQC|BAM_LIST File]])
* Single merged, recalibrated, and deduped BAM file for each subject (stored in a [[#BAM_LIST File for bamQC|BAM_LIST File]])
* BAI file for each subject
* Reference files
* Reference files
* (Optional) configuration file to override default options
* (Optional) configuration file to override default options
# sample id
# sample id
# comma separated population labels (optional column)
# comma separated population labels (optional column)
# BAM File (preferable to have full paths to BAM files)
# BAM File (preferable to have full path to BAM file)
# BAI File (preferable to have full path to BAI file)
[SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1]
[SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE] [BAI_FILE]
or
or
[SAMPLE_ID] [BAM_FILE1]
[SAMPLE_ID] [BAM_FILE] [BAI_FILE]
* Notes:
* Notes:
====Inputs====
====Inputs====
* Single merged, recalibrated, and deduped BAM file for each subject (stored in a [[#BAM_LIST File for bamQC|BAM_LIST File]])
* Single merged, recalibrated, and deduped BAM file for each subject (stored in a [[#BAM_LIST File for bamQC_createIndex|BAM_LIST File]])
* Reference files
* Reference files
* (Optional) configuration file to override default options
* (Optional) configuration file to override default options
=====BAM_LIST File for bamQC=====
=====BAM_LIST File for bamQC_createIndex=====
* Each line of the BAM list file represents a single individual
* Each line of the BAM list file represents a single individual
# BAM File (preferable to have full paths to BAM files)
# BAM File (preferable to have full paths to BAM files)
[SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1]
[SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE]
or
or
[SAMPLE_ID] [BAM_FILE1]
[SAMPLE_ID] [BAM_FILE]
* Notes:
* Notes:
====Outputs====
====Outputs====
Upon successful completion of the *bamQC* sub-pipeline, you should see the following files/subdirectories under the user specified output directory:
Upon successful completion of the *bamQC_createIndex* sub-pipeline, you should see the following files/subdirectories under the user specified output directory:
* A BAI file with the exact same path and name as the BAM file that was input, with *.bai on the end
* '''QCFiles/''' - contains quality control results
* '''QCFiles/''' - contains quality control results
** VerifyBamID Output - see [[VerifyBamID#A_guideline_to_interpret_output_files|VerifyBamID: A guideline to interpret output files]] for more information
** VerifyBamID Output - see [[VerifyBamID#A_guideline_to_interpret_output_files|VerifyBamID: A guideline to interpret output files]] for more information
*** '''''*/SAMPLE.qplot.stats'' - sample statistics'''
*** '''''*/SAMPLE.qplot.stats'' - sample statistics'''
You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *bamQC* sub-pipeline failed.
You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *bamQC_createIndex* sub-pipeline failed.
'''On success, the QCFiles/ folder contains the quality control output'''
'''On success, the QCFiles/ folder contains the quality control output'''
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
|-
| --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM_LIST File for bamQC|BAM_LIST File]] || $(OUT_DIR)/bam.list
| --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM_LIST File for bamQC_createIndex|BAM_LIST File]] || $(OUT_DIR)/bam.list
|-
|-
| --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)
==== Example Command Line ====
==== Example Command Line ====
gotcloud pipe –-name bamQC --numjobs <N>
gotcloud pipe –-name bamQC_createIndex --numjobs <N>
