GotCloud: Variant Calling Pipeline - Revision history

Kleckner: /* Running the Automatic Test */

2015-03-30T22:54:59Z

Running the Automatic Test

← Older revision		Revision as of 18:54, 30 March 2015
Line 18:		Line 18:
	** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run snpcall on your own samples.		** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run snpcall on your own samples.
	*Run <code>ldrefine</code> pipeline test:		*Run <code>ldrefine</code> pipeline test:
	gotcloud ~~snpcall~~ --test OUTPUT_DIR		gotcloud ldrefine --test OUTPUT_DIR
	** Where <code>OUTPUT_DIR</code> is the directory where you want to store the test results		** Where <code>OUTPUT_DIR</code> is the directory where you want to store the test results
	** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run ldrefine on your own samples.		** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run ldrefine on your own samples.

Mktrost: /* Running */

2015-03-06T18:23:00Z

Running

← Older revision		Revision as of 14:23, 6 March 2015
Line 97:		Line 97:
	== Variant Calling Command-line Options/Configuration Settings ==		== Variant Calling Command-line Options/Configuration Settings ==
	{{:GotCloud: Variant Calling Options}}		{{:GotCloud: Variant Calling Options}}


			== Use Cases & Recommended Settings ==
			=== Single Sample Processing ===
			To run single sample processing we recommend adding the following settings to your configuration file:
			UNIT_CHUNK = 20000000
			MODEL_GLFSINGLE = TRUE
			MODEL_SKIP_DISCOVER = FALSE
			MODEL_AF_PRIOR = TRUE
			VCF_EXTRACT = $(REF_DIR)/snpOnly.vcf.gz
			EXT = $(REF_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(REF_DIR)/chrCHR.filtered.sites.vcf.gz

			Explanation of these settings:
			* <code>UNIT_CHUNK</code> - since this is only 1 sample, process larger regions at a time than default
			* <code>MODEL_GLFSINGLE</code> - single sample, so model glfsingle
			* <code>MODEL_SKIP_DISCOVER</code> - do not skip the variant discovery step
			* <code>MODEL_AF_PRIOR</code> - use AF prior for genotyping
			* <code>VCF_EXTRACT</code> - VCF file to use for extracting the site information to genotype
			** This file is included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142\|hs37d5-db142]]
			* <code>EXT</code> - VCF reference files to use for the external filtering
			** These files are included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142\|hs37d5-db142]]

Mktrost: /* BAM List File */

2015-02-10T20:46:02Z

BAM List File

← Older revision		Revision as of 16:46, 10 February 2015
Line 62:		Line 62:
	*** 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.		*** 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.

	The path to the BAM List file is defaulted to the <code>outputDirectory/bam.list</code>. It can be overridden by setting <code>--bamlist</code>, <code>--bam_list</code>, or <code>--list</code> on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File.		The path to the BAM List file is defaulted to the <code>outputDirectory/bam.list</code>. It can be overridden by setting <code>--bamlist</code>, <code>--bam_list</code>, or <code>--list</code> on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File. See [[#Required_Options\|Required Options]] for more information.

	=== Reference Files ===		=== Reference Files ===

Mktrost: /* BAM List File */

2015-02-10T20:45:06Z

BAM List File

← Older revision		Revision as of 16:45, 10 February 2015
Line 61:		Line 61:
	*** only used by Thunder (part of ldrefine pipeline)		*** 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.		*** 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.

			The path to the BAM List file is defaulted to the <code>outputDirectory/bam.list</code>. It can be overridden by setting <code>--bamlist</code>, <code>--bam_list</code>, or <code>--list</code> on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File.

	=== Reference Files ===		=== Reference Files ===

Mktrost: /* Results */

2014-10-29T14:59:15Z

Results

← Older revision		Revision as of 10:59, 29 October 2014
Line 123:		Line 123:
	* glfs with a bams & samples subdirectory		* glfs with a bams & samples subdirectory
	* pvcfs with a subdirectory per chromosome and then per region		* pvcfs with a subdirectory per chromosome and then per region
	* split with a subdirectory per chromosome		* '''split''' with a subdirectory per chromosome
	* vcfs with a subdirectory per chromosome		* '''vcfs''' with a subdirectory per chromosome
	* (optionally your target directory)		* (optionally your target directory)

	Under the vcf/chrXX directory, there should be:		Under the '''vcf/chrXX''' directory, there should be:
	* chrXX.filtered.sites.vcf		* chrXX.filtered.sites.vcf
	* chrXX.filtered.sites.vcf.norm.log		* chrXX.filtered.sites.vcf.norm.log
	* chrXX.filtered.sites.vcf.summary		* chrXX.filtered.sites.vcf.summary
	* chrXX.filtered.vcf.gz		* '''chrXX.filtered.vcf.gz''' - final filtered variant call file
	* chrXX.filtered.vcf.gz.OK		* chrXX.filtered.vcf.gz.OK
	* chrXX.filtered.vcf.gz.tbi		* chrXX.filtered.vcf.gz.tbi
Line 149:		Line 149:
	The filtered is the merged.vcf after it has been run through filters and is marked with PASS/FAIL.		The filtered is the merged.vcf after it has been run through filters and is marked with PASS/FAIL.

	Under the split/chrXX directory, there should be:		Under the '''split/chrXX''' directory, there should be:
	* chrXX.filtered.PASS.split.[N].vcf.gz		* chrXX.filtered.PASS.split.[N].vcf.gz
	* chrXX.filtered.PASS.split.err		* chrXX.filtered.PASS.split.err
	* chrXX.filtered.PASS.split.vcflist		* chrXX.filtered.PASS.split.vcflist
	* chrXX.filtered.PASS.gz		* '''chrXX.filtered.PASS.gz''' - final variant call file with only PASS variants
	* subset.OK		* subset.OK

Mktrost at 14:56, 29 October 2014

2014-10-29T14:56:15Z

@@ Line 79: / Line 79: @@
 {{:GotCloud: Configuration}}
-====Additional User Config Files Settings====
+See [[#Variant Calling Command-line Options/Configuration Settings|Variant Calling Command-line Options/Configuration Settings]] for more information on Configuration options.
-====Targeted/Exome Sequencing Settings====
+==== Example Configuration File ====
 Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5
   CHRS = 20 22
@@ Line 134: / Line 91: @@
   HM3_VCF = $(REF_DIR)/hapmap3_r3_b37.sites.vcf.gz
   DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz
 == Running ==

Mktrost: /* Additional Required User Config Files Settings */

2014-10-24T14:17:47Z

Additional Required User Config Files Settings

← Older revision		Revision as of 10:17, 24 October 2014
Line 79:		Line 79:
	{{:GotCloud: Configuration}}		{{:GotCloud: Configuration}}

	====Additional ~~Required~~ User Config Files Settings====		====Additional User Config Files Settings====
	{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"		{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
	! Configuration Key !! Command-line Flag !! Value Description !! Default Value		! Configuration Key !! Command-line Flag !! Value Description !! Default Value

Mktrost: /* Running */

2014-10-23T22:54:05Z

Running

← Older revision		Revision as of 18:54, 23 October 2014
Line 148:		Line 148:
	* Replace <code>2</code> following <code>--numjobs</code> with the number of jobs to be run in parallel		* Replace <code>2</code> following <code>--numjobs</code> with the number of jobs to be run in parallel
	* If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.		* If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.


	=== Running on a Cluster ===		=== Running on a Cluster ===

Mktrost: /* Example Configuration File */

2014-10-23T22:49:19Z

Example Configuration File

← Older revision		Revision as of 18:49, 23 October 2014
Line 126:		Line 126:
	=== Example Configuration File ===		=== Example Configuration File ===
	Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5		Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5
	CHRS = ~~1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19~~ 20 21 22		CHRS = 20 22
	~~BAM_INDEX~~ = /path~~/freeze5~~/freeze5.bam.~~index ### The BAM index file described above~~		BAM_LIST = /path/freeze5.bam.list
	OUT_DIR = /path/freeze5/~~output ### Directory in which to put all gotcloud~~ output		OUT_DIR = /path/freeze5/output
	~~REF~~ = /path/reference/hs37d5.fa ~~### Reference sequence~~		REF_DIR = /path/reference/
	INDEL_PREFIX = ~~/path/reference~~/1kg.pilot_release.merged.indels.sites.hg19 ~~### Known indel sites~~		REF = $(REF_DIR)/hs37d5.fa
	HM3_VCF = ~~/path/reference~~/hapmap3_r3_b37.sites.vcf.gz ~~### HapMap variants (requires tabix index file in same directory)~~		INDEL_PREFIX = $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19
	DBSNP_VCF = ~~/path/reference~~/dbsnp_135.b37.sites.vcf.gz ~~### dbSNP variants (requires tabix index file in same directory)~~		HM3_VCF = $(REF_DIR)/hapmap3_r3_b37.sites.vcf.gz
			DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz

	== Running ==		== Running ==

Mktrost: /* Chromosome X Calling */

2014-10-23T22:47:12Z

Chromosome X Calling

← Older revision		Revision as of 18:47, 23 October 2014
Line 114:		Line 114:
	==== Chromosome X Calling ====		==== Chromosome X Calling ====
	For proper Chromosome X calling, it is recommended to specify a PED file with sex information:		For proper Chromosome X calling, it is recommended to specify a PED file with sex information:
	* PED_INDEX ~~= pedfile.~~ped		{\| 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:		Format of PED file: