GotCloud: Alignment Sub-Pipelines - Revision history

Kleckner: /* Example Command Line */

2015-03-19T01:37:18Z

Example Command Line

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	==== Example Command Line ====		==== Example Command Line ====
	gotcloud pipe –-name ~~bamQC~~ --numjobs <N>		gotcloud pipe –-name bamQC_createIndex --numjobs <N>

Kleckner: /* Command-Line and Configuration Options */

2015-03-19T01:36:09Z

Command-Line and Configuration Options

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	! 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)

Kleckner: /* Inputs */

2015-03-19T01:35:58Z

Inputs

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	====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

Kleckner: /* BAM_LIST File for bamQC */

2015-03-19T01:35:44Z

BAM_LIST File for bamQC

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	* (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

Kleckner: /* Outputs */

2015-03-19T01:35:22Z

Outputs

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	*** '''''*/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'''

Kleckner: /* Outputs */

2015-03-19T01:34:47Z

Outputs

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	====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

Kleckner: /* BAM_LIST File for bamQC */

2015-03-19T01:33:31Z

BAM_LIST File for bamQC

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	# 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:

Kleckner: /* BAM_LIST File for bamQC */

2015-03-19T01:32:09Z

BAM_LIST File for bamQC

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	# 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:

Kleckner: /* Inputs */

2015-03-19T01:30:05Z

Inputs

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	====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

Kleckner: /* bamQC_createIndex */

2015-03-19T01:29:26Z

bamQC_createIndex

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	== bamQC_createIndex ==		== bamQC_createIndex ==
			*What it does:
			# creates a BAI file for any BAM that is missing it
			# qplot
			# verifyBamID

			====Inputs====
			* Single merged, recalibrated, and deduped BAM file for each subject (stored in a [[#BAM_LIST File for bamQC\|BAM_LIST File]])
			* Reference files
			* (Optional) configuration file to override default options

			=====BAM_LIST File for bamQC=====
			* Each line of the BAM list file represents a single individual

			Columns:
			# sample id
			# comma separated population labels (optional column)
			# BAM File (preferable to have full paths to BAM files)

			[SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1]
			or
			[SAMPLE_ID] [BAM_FILE1]

			* Notes:
			** tab delimited
			** population label is optional - it will default to <code>ALL</code>
			*** only used by Thunder (part of ldrefine pipeline)
			*** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample.

			====Outputs====
			Upon successful completion of the bamQC sub-pipeline, you should see the following files/subdirectories under the user specified output directory:

			* '''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
			*** ''*/SAMPLE.genoCheck.depthRG'' - depth distribution of the sequence reads per read group
			*** ''*/SAMPLE.genoCheck.depthSM'' - depth distribution of the sequence reads per sample
			*** ''*/SAMPLE.genoCheck.err'' - log file
			*** ''*/SAMPLE.genoCheck.log'' - log file
			*** ''*/SAMPLE.genoCheck.OK'' - temp file indicating the VerifyBAMID step completed successfully
			*** ''*/SAMPLE.genoCheck.selfRG'' - per-readGroup statistics describing how well each lane matches to the annotated sample
			*** '''''*/SAMPLE.genoCheck.selfSM'' - main output file containing the contamination estimate; per-sample statistics describing how well the sample matches to the annotated sample'''
			**** Check the 'FREEMIX' column for genotype-free estimate of contamination 0-1 scale, the lower, the better
			**** If [FREEMIX] >= 0.03 and [FREELK1]-[FREELK0] is large, possible contamination
			** Qplot Output - see: [[QPLOT#Diagnose_sequencing_quality\|QPLOT: Diagnose sequencing quality]] for more info on how to use QPLOT results
			*** ''*/SAMPLE.qplot.OK'' - temp file indicating the qplot step completed successfully
			*** '''''*/SAMPLE.qplot.R'' - Rscript that can be used to generate the pdf graphs'''
			*** '''''*/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.

			'''On success, the QCFiles/ folder contains the quality control output'''

			===Command-Line and Configuration Options===

			*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
			\|-
			\| --list/--bam_list/--bamlist ''file'' \|\| BAM_LIST \|\| path to the [[#BAM_LIST File for bamQC\|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"
			! Command-line Flag !! Configuration Key !! Value Description !! Default Value
			\|-
			\| --outdir ''path'' \|\| OUT_DIR \|\| output directory \|\|
			\|-
			\| --conf ''file'' \|\| \|\| configuration file to use \|\|
			\|-
			\| \|\| REF_DIR \|\| where the reference/resource files are stored \|\| gotcloud.ref subdirectory within the base GotCloud directory
			\|-
			\| \|\| REF \|\| [[GotCloud: Genetic Reference and Resource Files#Reference fasta Files\|Reference fasta Files]] \|\| $(REF_DIR)/human.g1k.v37.fa
			\|-
			\| \|\| DBSNP_VCF \|\| [[GotCloud: Genetic Reference and Resource Files#DBSNP VCF File\|DBSNP VCF Files]] \|\| $(REF_DIR)/dbsnp_135.b37.vcf.gz
			\|-
			\| \|\| HM3_VCF \|\| [[GotCloud: Genetic Reference and Resource Files#HapMap3 VCF File\|HapMap3 VCF Files]] \|\| $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz
			\|}

			==== Example Configuration File ====
			Example configuration file where reference files happen to be stored in /path/reference, and bam list file is stored in in path/freeze5
			BAM_LIST = /path/freeze5.bam.list
			OUT_DIR = /path/freeze5/output
			REF_DIR = /path/reference/
			REF = $(REF_DIR)/hs37d5.fa
			DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz
			HM3_VCF = $(REF_DIR)/hapmap3_r3_b37.sites.vcf.gz

			==== Example Command Line ====
			gotcloud pipe –-name bamQC --numjobs <N>