RealSFS - Revision history

Thorfinn at 11:20, 26 June 2022

2022-06-26T11:20:36Z

← Older revision		Revision as of 13:20, 26 June 2022
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	<pre>		<pre>
	#1d sfs		#1d sfs
	./realSFS afile.saf.idx [-~~start~~ FNAME -P nThreads -tole tole -maxIter -nSites ]		./realSFS afile.saf.idx [-sfs FNAME -P nThreads -tole tole -maxIter -nSites ]
	#2dsfs		#2dsfs
	./realSFS pop1.saf.idx pop2.saf.idx [-~~start~~ FNAME -P nThreads -tole tole -maxIter -nSites]		./realSFS pop1.saf.idx pop2.saf.idx [-sfs FNAME -P nThreads -tole tole -maxIter -nSites]
	#3dsfs		#3dsfs
	./realSFS pop1.saf.idx pop2.saf.idx pop3.saf.idx [-~~start~~ FNAME -P nThreads -tole tole -maxIter -nSites]		./realSFS pop1.saf.idx pop2.saf.idx pop3.saf.idx [-sfs FNAME -P nThreads -tole tole -maxIter -nSites]
	</pre>		</pre>
	The saf files are generated using [[SFS estimation\| ./angsd -doSaf]].		The saf files are generated using [[SFS estimation\| ./angsd -doSaf]].
	;-start is a file containing a ~~log scaled estimate~~ of the SFS that can be used as the start point for the EM optimisation.		;-start is a file containing a the expected values of the SFS that can be used as the start point for the EM optimisation.
	;-tole When the difference in successive likelihood values in the EM algorithm gets below this value the optimisation will stop		;-tole When the difference in successive likelihood values in the EM algorithm gets below this value the optimisation will stop
	;-P number of threads to allocate to program		;-P number of threads to allocate to program

2016-07-15T11:11:46Z

Using NGStools/NGSpopgen

← Older revision		Revision as of 13:11, 15 July 2016
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	This will then generate a single '''shared.pos.gz''' file, and a '''.saf''' file for each saf file. The output will only be generated for the sites that exists in all populations.		This will then generate a single '''shared.pos.gz''' file, and a '''.saf''' file for each saf file. The output will only be generated for the sites that exists in all populations.

			=Merge SAF files=
			<pre>
			./realSFS cat
			-> This will cat together .saf files from angsd
			-> regions has to be disjoint between saf files. This WONT be checked (alot) !
			-> This has only been tested on safs for different chrs !
			-> outnames: '(null)' number of safe:0
			</pre>

2016-07-15T11:11:17Z

← Older revision		Revision as of 13:11, 15 July 2016
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	* You can also supply -sites directly to the realSFS subprogram for choosing a subset of sites. This could be useful if you are interested in the spectra for differenct functional categories.		* You can also supply -sites directly to the realSFS subprogram for choosing a subset of sites. This could be useful if you are interested in the spectra for differenct functional categories.

			* You can also merge saf files. Then you can run angsd on the separate chromosomes and merge afterwars

	See also [[SFS Estimation]] and [[2d SFS Estimation]].		See also [[SFS Estimation]] and [[2d SFS Estimation]].

2016-03-02T12:01:28Z

← Older revision		Revision as of 14:01, 2 March 2016
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	* you can also estimate fst and pbs with realSFS see [[Fst PCA]].		* you can also estimate fst and pbs with realSFS see [[Fst PCA]].

			* You can also supply -sites directly to the realSFS subprogram for choosing a subset of sites. This could be useful if you are interested in the spectra for differenct functional categories.

	See also [[SFS Estimation]] and [[2d SFS Estimation]].		See also [[SFS Estimation]] and [[2d SFS Estimation]].

2015-12-04T12:53:23Z

Brief overview

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 See also [[SFS Estimation]] and [[2d SFS Estimation]].
 =Brief overview=
 ==Estimating SFS==
 <pre>

2015-12-04T12:52:34Z

← Older revision		Revision as of 14:52, 4 December 2015
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	~~<pre>~~
	* The program was called emOptim2 in earlier versions, this has now been changed to the more appropiate: 'realSFS'
	~~</pre>~~

	* This program will estimate the (multi) SFS based on a .saf file generated from the '''./angsd [options] -doSaf '''.		* This program will estimate the (multi) SFS based on a .saf file generated from the '''./angsd [options] -doSaf '''.

2015-07-22T16:57:14Z

← Older revision		Revision as of 18:57, 22 July 2015
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	* This program will estimate the (multi) SFS based on a .saf file generated from the '''./angsd [options] -doSaf '''.		* This program will estimate the (multi) SFS based on a .saf file generated from the '''./angsd [options] -doSaf '''.

	* It can also textoutput the saf files		* It can also textoutput the saf files.

	* It can also convert to the old format		* It can also convert to the old format.

	* You can also specify regions of analysis using -r chromoname:start-stop		* You can also specify regions of analysis using -r chromoname:start-stop

	* you can also estimate fst and pbs with realSFS see [[Fst PCA]]		* you can also estimate fst and pbs with realSFS see [[Fst PCA]].

	See also [[SFS Estimation]] and [[2d SFS Estimation]].		See also [[SFS Estimation]] and [[2d SFS Estimation]].

2015-07-22T16:57:01Z

← Older revision		Revision as of 18:57, 22 July 2015
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	* You can also specify regions of analysis using -r chromoname:start-stop		* You can also specify regions of analysis using -r chromoname:start-stop

	* you can also estimate fst and pbs with realSFS see [[Fst & PCA]]		* you can also estimate fst and pbs with realSFS see [[Fst PCA]]

	See also [[SFS Estimation]] and [[2d SFS Estimation]].		See also [[SFS Estimation]] and [[2d SFS Estimation]].

2015-07-22T16:56:44Z

← Older revision		Revision as of 18:56, 22 July 2015
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	* You can also specify regions of analysis using -r chromoname:start-stop		* You can also specify regions of analysis using -r chromoname:start-stop

			* you can also estimate fst and pbs with realSFS see [[Fst & PCA]]

	See also [[SFS Estimation]] and [[2d SFS Estimation]].		See also [[SFS Estimation]] and [[2d SFS Estimation]].

2015-07-22T16:52:59Z

2dsfs

← Older revision		Revision as of 18:52, 22 July 2015
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	So each line in your Whit.saf.ml, is an SFS for a region.		So each line in your Whit.saf.ml, is an SFS for a region.

	=2dsfs=		=Estimating 2dsfs=
	<pre>		<pre>
	./realSFS pop1.saf.idx pop2.saf.idx[-start FNAME -P nThreads -tole tole -maxIter -nSites ]		./realSFS pop1.saf.idx pop2.saf.idx[-start FNAME -P nThreads -tole tole -maxIter -nSites ]