Filters - Revision history

Thorfinn: /* Number of non missing individuals */

2019-11-15T06:49:14Z

Number of non missing individuals

← Older revision		Revision as of 08:49, 15 November 2019
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	; -minInd [int]: Only keep sites with at least minIndDepth (default is 1) from at least [int] individuals		; -minInd [int]: Only keep sites with at least minIndDepth (default is 1) from at least [int] individuals

	~~; -setMinDepthInd [int]: Only works with the -minInd filter. Change the minimum depth the individuals must have in order to keep the site. Default is 1.~~

	=Extra=		=Extra=

2019-11-15T06:48:52Z

Number of non missing individuals

← Older revision		Revision as of 08:48, 15 November 2019
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	; -minInd [int]: Only keep sites with at least minIndDepth (default is 1) from at least [int] individuals		; -minInd [int]: Only keep sites with at least minIndDepth (default is 1) from at least [int] individuals

	; -~~minIndDepth~~ [int]: Only works with the -minInd filter. Change the minimum depth the individuals must have in order to keep the site. Default is 1.		; -setMinDepthInd [int]: Only works with the -minInd filter. Change the minimum depth the individuals must have in order to keep the site. Default is 1.

	=Extra=		=Extra=

2017-03-03T10:16:52Z

Number of non missing individuals

← Older revision		Revision as of 12:16, 3 March 2017
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	; -minInd [int]: ~~only work with~~ sites with ~~information~~ from at least [int] individuals		; -minInd [int]: Only keep sites with at least minIndDepth (default is 1) from at least [int] individuals

			; -minIndDepth [int]: Only works with the -minInd filter. Change the minimum depth the individuals must have in order to keep the site. Default is 1.

	=Extra=		=Extra=

2017-03-03T09:58:29Z

Extra

← Older revision		Revision as of 11:58, 3 March 2017
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	;-setMaxDepthInd [int]:		;-setMaxDepthInd [int]:
	Discard individual if sequencing depth for an individual is above [int] This filter is only applied to analysis which are based on counts of alleles i.e. analysis that uses [[Alleles counts \| -doCounts]]		Discard individual if sequencing depth for an individual is above [int] This filter is only applied to analysis which are based on counts of alleles i.e. analysis that uses [[Alleles counts \| -doCounts]]
	~~[[Alleles counts \| -doCounts]]~~

2017-03-03T09:56:04Z

Extra

← Older revision		Revision as of 11:56, 3 March 2017
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	=Extra=		=Extra=
	;-setMinDepth [int]:		;-setMinDepth [int]:
	Discard site if total sequencing depth (all individuals added together) is below [int]		Discard site if total sequencing depth (all individuals added together) is below [int].
	Requires [[Alleles counts \| -doCounts]]		Requires [[Alleles counts \| -doCounts]]

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	;-setMinDepthInd [int]:		;-setMinDepthInd [int]:
	Discard individual if sequencing depth for an individual is below [int]		Discard individual if sequencing depth for an individual is below [int]. This filter is only applied to analysis which are based on counts of alleles i.e. analysis that uses [[Alleles counts \| -doCounts]]
	~~Requires~~ [[Alleles counts \| -doCounts]]

	;-setMaxDepthInd [int]:		;-setMaxDepthInd [int]:
	Discard individual if sequencing depth for an individual is above [int]		Discard individual if sequencing depth for an individual is above [int] This filter is only applied to analysis which are based on counts of alleles i.e. analysis that uses [[Alleles counts \| -doCounts]]
	[[Alleles counts \| -doCounts]]		[[Alleles counts \| -doCounts]]

2017-01-24T12:39:01Z

Selected Sites

← Older revision		Revision as of 14:39, 24 January 2017
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	=Selected Sites=		=Selected Sites=
	For analysing specfic regions see [[Input#BAM_files]]. If you are interested in running your analysis at individual sites that are distributed throughout the entire genome, it might be faster to simply to loop over the entire data, but only analyse the data at specific positions. This can be done by supplying the [[Sites \| -sites]] argument. With this approach we also allows for the forcing of major/minor alleles using external information.		For analysing specfic regions see [[Input#BAM_files]]. If you are interested in running your analysis at individual sites that are distributed throughout the entire genome, it might be faster to simply to loop over the entire data, but only analyse the data at specific positions. This can be done by supplying the [[Sites \| -sites]] argument. With this approach we also allows for the forcing of major/minor alleles using external information.

	=Allele frequencies=		=Allele frequencies=

2016-09-05T15:32:39Z

Extra

← Older revision		Revision as of 17:32, 5 September 2016
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	;-setMinDepthInd [int]:		;-setMinDepthInd [int]:
	Discard ~~site~~ if sequencing depth for an individual is below [int]		Discard individual if sequencing depth for an individual is below [int]
	Requires [[Alleles counts \| -doCounts]]		Requires [[Alleles counts \| -doCounts]]

	;-setMaxDepthInd [int]:		;-setMaxDepthInd [int]:
	Discard ~~site~~ if sequencing depth for an individual is above [int]		Discard individual if sequencing depth for an individual is above [int]
	[[Alleles counts \| -doCounts]]		[[Alleles counts \| -doCounts]]

2016-03-02T12:04:45Z

Extra

@@ Line 43: / Line 43: @@
 Discard site if total sequencing depth (all individuals added together) is above [int]
 [[Alleles counts | -doCounts]]
 ;-geno_minDepth [int]

2015-12-04T15:11:19Z

Extra

← Older revision		Revision as of 17:11, 4 December 2015
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	Discard site if total sequencing depth (all individuals added together) is above [int]		Discard site if total sequencing depth (all individuals added together) is above [int]
	[[Alleles counts \| -doCounts]]		[[Alleles counts \| -doCounts]]


	;-geno_minDepth [int]		;-geno_minDepth [int]

2015-12-04T15:11:09Z

Extra

← Older revision		Revision as of 17:11, 4 December 2015
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	This requires [[Alleles counts \| -doCounts]] and [[Genotype calling \|-doGeno ]]		This requires [[Alleles counts \| -doCounts]] and [[Genotype calling \|-doGeno ]]

	~~;-trim [int]~~
	~~Removes the [int] bases in both 'ends' of the reads, mostly useful for ancient DNA.~~

	=Examples=		=Examples=