GotCloud: Variant Calling Options - Revision history

Mktrost: /* Chromosome X Calling */

2015-02-11T18:57:44Z

Chromosome X Calling

← Older revision		Revision as of 14:57, 11 February 2015
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	\|}		\|}

	==== Chromosome X Calling ====		==== Chromosome X/Y Calling ====
	For proper Chromosome X calling, it is recommended to specify a PED file with sex information:		For proper Chromosome X/Y 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"		{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
	! Configuration Key !! Value Description		! Configuration Key !! Value Description

Mktrost: /* Hard Filtering Options */

2014-10-29T14:52:42Z

Hard Filtering Options

← Older revision		Revision as of 10:52, 29 October 2014
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	* To remove any filter, set it to blank in your configuration file		* To remove any filter, set it to blank in your configuration file

			For additional hard filter information, see: [[GotCloud: Filters]]

	'''Basic per variant filters:'''		'''Basic per variant filters:'''
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	! Filter !! Configuration Key !! VCF value checked !! Filter Variants with... !! Default Value		! Filter !! Configuration Key !! VCF value checked !! Filter Variants with... !! Default Value
	\|-		\|-
	\| max depth \|\| FILTER_MAX_SAMPLE_DP \|\| rowspan="2" \|INFO:DP \|\| > ''conf value'' * total number of samples \|\| 1000		\| max depth \|\| FILTER_MAX_SAMPLE_DP \|\| rowspan="2" \|INFO:DP \|\| > ''conf value'' * total number of samples \|\| 1000[[
	\|-		\|-
	\| min depth \|\|FILTER_MIN_SAMPLE_DP \|\| < ''conf value'' * total number of samples \|\| 1		\| min depth \|\|FILTER_MIN_SAMPLE_DP \|\| < ''conf value'' * total number of samples \|\| 1

Mktrost: /* Hard Filtering Options */

2014-10-29T14:15:23Z

Hard Filtering Options

@@ Line 332: / Line 332: @@
 | colspan="3" | total number of samples between min & max, use logscale
 |-
-| colspan="3" |
+|}
 |-
-! colspan="3" | Filters
+| max Cycle Bias Peason's correlation || FILTER_MAX_CBR || INFO:CBR || > ''conf value''/100.0 || 20, 10 || < 100
 |-
-! Filter !! Configuration Key !! VCF value checked !! Filter Variants with... !! Default Value
+| max LQR || FILTER_MAX_LQR || INFO:LQR || > ''conf value''/100.0 || 30, 20 || < 100
 |-
 |}

Mktrost: /* Hard Filtering Options */

2014-10-28T21:21:28Z

Hard Filtering Options

@@ Line 293: / Line 293: @@
 ==== Hard Filtering Options ====
 {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
-! Configuration Key !! Program Description !! Default Value
+! colspan="3" | Configuration settings for min/max # samples to determine filter value when the filter setting contains multiple values separated by ',' or ' '
 |-
-| FILTER_ADDITIONAL ||  ||
+! Filter !! Configuration Key !! VCF value checked !! Filter Variants with... !! Default Value
 |-
@@ Line 318: / Line 357: @@
 |}

Mktrost at 19:51, 28 October 2014

2014-10-28T19:51:40Z

← Older revision		Revision as of 15:51, 28 October 2014
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	*''produce an error if reads overlap multiple targeted regions''		*''produce an error if reads overlap multiple targeted regions''
	** see: [[GotCloud: FAQs#Targetted/Exome\|GotCloud: FAQs->Targetted/Exome]]		** see: [[GotCloud: FAQs#Targetted/Exome\|GotCloud: FAQs->Targetted/Exome]]
			\|-
			\| WGS_SVM \|\| whether or not to run SVM on the whole genome rather than by chromosome (default is by chromosome). Set to TRUE if you are running with a small number of target regions. \|\|
			\|-
	\|}		\|}

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	{\| 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 !! Program Description !! Default Value		! Configuration Key !! Program Description !! Default Value
			\|-
			\| WGS_SVM \|\| whether or not to run SVM on the whole genome rather than by chromosome (default is by chromosome). Set to TRUE if you are running with a small number of target regions. \|\|
	\|-		\|-
	\| VCF_EXTRACT \|\| position file to use for glfFlex \|\|		\| VCF_EXTRACT \|\| position file to use for glfFlex \|\|
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	\|}		\|}

	==== Options ====		==== Additional Options ====

	{\| 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"
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	\|-		\|-

	~~\| \|~~\| SAMTOOLS_VIEW_FILTER \|\| filter settings for samtools view (default filters by mapping quality and flag) \|\| -q 20 -F 0x0704		\| SAMTOOLS_VIEW_FILTER \|\| filter settings for samtools view (default filters by mapping quality and flag) \|\| -q 20 -F 0x0704
	\|-
	~~\| \|\| NOBAQ_SUBSTRINGS \|\| skip the BAQ step if the BAM filename contains the specified space-separated substrings \|\| SOLID~~
	\|-
	~~\| \|\| BAM_DEPEND \|\| set to true to rerun the pipeline if the BAM files are newer than previously run steps that use them \|\| FALSE~~
	\|-		\|-
	\| \|\| ~~WGS_SVM \|\|~~ \|\|		\| NOBAQ_SUBSTRINGS \|\| skip the BAQ step if the BAM filename contains the specified space-separated substrings \|\| SOLID
	\|-		\|-
	\| \|\| ~~MAKE_OPTS \|\|~~ \|\|		\| BAM_DEPEND \|\| set to true to rerun the pipeline if the BAM files are newer than previously run steps that use them \|\| FALSE
	\|-		\|-
	\| \|\| ~~KEEP_LOG \|\|~~ \|\|		\| MAKE_OPTS \|\| set to add additional makefile options \|\|
	\|-		\|-
	\|}		\|}

Mktrost: /* Options */

2014-10-28T19:47:26Z

Options

← Older revision		Revision as of 15:47, 28 October 2014
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	\|}		\|}

	==== Options ====		==== GlfFlex Options ====

	{\| 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 !! Program Description !! Default Value		! Configuration Key !! Program Description !! Default Value
	\|-		\|-
			\| VCF_EXTRACT \|\| position file to use for glfFlex \|\|
	\| \|\| ~~SAMTOOLS_VIEW_FILTER \|\|~~ \|\|
	\|-		\|-
	\| \|\| ~~NOBAQ_SUBSTRINGS \|\| skip the BAQ step~~ if ~~the BAM filename contains the specified space-separated substrings~~ \|\| ~~SOLID~~		\| MODEL_GLFSINGLE \|\| set to TRUE if glfSingle model should be used for glfFlex \|\|
	\|-		\|-
	\| \|\| ~~MODEL_GLFSINGLE \|\|~~ \|\|		\| MODEL_SKIP_DISCOVER \|\| set to true to disable variant discovery for glfFlex \|\|
	\|-		\|-
	\| \|\| ~~MODEL_SKIP_DISCOVER \|\|~~ \|\|		\| MODEL_AF_PRIOR \|\| set to true to use AF prior for genotyping for glfFlex \|\|
	\|-		\|-
	\| \|~~\| MODEL_AF_PRIOR \|\| \|\|~~		\|}


			==== SVM Filtering Options ====
			{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
			! Configuration Key !! Program Description !! Default Value
	\|-		\|-
	\| \|\| ~~BAM_DEPEND \|\|~~ \|\|		\| POS_SAMPLE \|\| percentage of positive samples used for training \|\| 100
	\|-		\|-
	\| \|\| ~~WGS_SVM \|\|~~ \|\|		\| NEG_SAMPLE \|\| percentage of negative samples used for training \|\| 100
	\|-		\|-
	\| \|\| ~~MAKE_OPTS \|\|~~ \|\|		\| SVM_CUTOFF \|\| SVM score cutoff for PASS/FAIL \|\| 0
	\|-		\|-
	~~\| \|~~\| USE_SVMMODEL \|\| \|\|		\| USE_SVMMODEL \|\| whether to use pre-trained model for SVM filtering \|\| FALSE
	\|-		\|-
	\| ~~SVM_CUTOFF~~ \|\| \|\|		\| SVMMODEL \|\| pre-trained model file (if USE_SVMMODEL is set to TRUE) \|\|
	\|-		\|-
	\| ~~SVMMODEL \|\| \|\|~~		\|}
	\|-
	~~\| \|\| POS_SAMPLE \|\| \|\|~~
	\|-		==== Hard Filtering Options ====
	~~\| \|\| NEG_SAMPLE \|\| \|\|~~
	\|-		{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
	~~\| \|\| KEEP_LOG \|\| \|\|~~		! Configuration Key !! Program Description !! Default Value
	\|-		\|-
	~~\| \|~~\| FILTER_ADDITIONAL \|\| \|\|		\| FILTER_ADDITIONAL \|\| \|\|
	\|-		\|-

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			\|}

			==== Options ====

			{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
			! Configuration Key !! Program Description !! Default Value
			\|-

			\| \|\| SAMTOOLS_VIEW_FILTER \|\| filter settings for samtools view (default filters by mapping quality and flag) \|\| -q 20 -F 0x0704
			\|-
			\| \|\| NOBAQ_SUBSTRINGS \|\| skip the BAQ step if the BAM filename contains the specified space-separated substrings \|\| SOLID
			\|-
			\| \|\| BAM_DEPEND \|\| set to true to rerun the pipeline if the BAM files are newer than previously run steps that use them \|\| FALSE
			\|-
			\| \|\| WGS_SVM \|\| \|\|
			\|-
			\| \|\| MAKE_OPTS \|\| \|\|
			\|-
			\| \|\| KEEP_LOG \|\| \|\|
			\|-
	\|}		\|}

Mktrost: /* Analysis Region Options */

2014-10-28T14:35:38Z

Analysis Region Options

← Older revision		Revision as of 10:35, 28 October 2014
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	=== Analysis Region Options ===		=== Analysis Region Options ===
			See [[#Targeted/Exome Sequencing Settings\|Targeted/Exome Sequencing Settings]] for more information on specifying exome/targetted regions and other 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"
	! Command-line Flag !! Configuration Key !! Value Description !! Default Value		! Command-line Flag !! Configuration Key !! Value Description !! Default Value

Mktrost: /* Analysis Region Options */

2014-10-24T18:29:30Z

Analysis Region Options

← Older revision		Revision as of 14:29, 24 October 2014
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	format (-end is optional): chr:start-end		format (-end is optional): chr:start-end
	\|		\|
			\|-
			\| \|\| UNIT_CHUNK \|\| chunk size of SNP calling (GotCloud breaks up each chromosome into regions of this size) \|\| 5000000
			\|-
			\| \|\| LD_NSNPS \|\| chunk size (number of SNPs) of genotype refinement \|\| 10000
			\|-
			\| \|\| LD_OVERLAP \|\| overlapping # of SNPs between chunks for genotype refinement \|\| 1000
			\|-
	\|}		\|}

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	** see: [[GotCloud: FAQs#Targetted/Exome\|GotCloud: FAQs->Targetted/Exome]]		** see: [[GotCloud: FAQs#Targetted/Exome\|GotCloud: FAQs->Targetted/Exome]]
	\|}		\|}



	=== Path Options ===		=== Path Options ===

Mktrost: /* Miscellaneous Options */

2014-10-24T18:28:53Z

Miscellaneous Options

Show changes

Mktrost at 16:10, 24 October 2014

2014-10-24T16:10:50Z

@@ Line 43: / Line 43: @@
 | --verbose ||  || Add additional messages when reading configuration ||
 |}
 === Analysis Region Options ===
@@ Line 54: / Line 57: @@
+|
 |}
 === Path Options ===