SFS Estimation - Revision history

Isin: Minor fix: Add missing /pre

2023-12-08T14:22:15Z

Minor fix: Add missing /pre

← Older revision		Revision as of 16:22, 8 December 2023
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	but the 'Incorporating deviations from Hardy-Weinberg Equilibrium (HWE)' section of that paper.		but the 'Incorporating deviations from Hardy-Weinberg Equilibrium (HWE)' section of that paper.

			</pre>

	{{#mermaid:graph LR;		{{#mermaid:graph LR;

Isin: Remove old yuml diagram and replace with mermaid equivalent

2023-12-08T14:21:30Z

Remove old yuml diagram and replace with mermaid equivalent

← Older revision		Revision as of 16:21, 8 December 2023
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	but the 'Incorporating deviations from Hardy-Weinberg Equilibrium (HWE)' section of that paper.		but the 'Incorporating deviations from Hardy-Weinberg Equilibrium (HWE)' section of that paper.

	~~</pre>~~
	~~<classdiagram type="dir~~:LR">		{{#mermaid:graph LR;
	[sequence data~~{bg:orange}~~]->GL[genotype likelihoods\|SAMtools;GATK;SOAPsnp;Kim et.al]		A[sequence data] --> B[genotype likelihoods<br/>- SAMtools<br/>- GATK<br/>- SOAPsnp<br/>- Kim et.al]
	~~[genotype likelihoods\|SAMtools;GATK;SOAPsnp;Kim et.al]~~->doSaf[.saf file~~{bg:blue}~~]		B -->\|doSaf\| C[.saf file]
	~~[.saf file{bg:blue}]~~->optimize('realSFS')[.saf.ml file~~{bg~~:~~red~~}]		C -->\|optimize realSFS\| D[.saf.ml file]
	~~</classdiagram>~~
			class A sequenceData;
			class B genotypeLikelihoods;
			class C safFile;
			class D safMlFile;

			classDef sequenceData fill:#FFA500;
			classDef genotypeLikelihoods fill:#FFFFFF;
			classDef safFile fill:#009FFF;
			classDef safMlFile fill:#FF0000;
			}}


	=Brief Overview=		=Brief Overview=

Thorfinn: /* Brief Overview */

2021-08-18T09:10:19Z

Brief Overview

← Older revision		Revision as of 11:10, 18 August 2021
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	=Brief Overview=		=Brief Overview=
	<pre>		<pre>
	./angsd -~~doSaf~~		./angsd -dosaf
	-> angsd version: 0.~~910~~-76-~~gad32889~~ (htslib: 1.3-32-~~gecdc348~~) build(~~Mar~~ ~~2 2016 12~~:38:33)		-> angsd version: 0.935-44-g02a07fc-dirty (htslib: 1.12-1-g9672589) build(Jul 8 2021 08:04:55)
	-> Analysis helpbox/synopsis information:		-> ./angsd -dosaf
	-> ~~Command~~:		-> Analysis helpbox/synopsis information:
	~~./angsd -doSaf~~ -> ~~Wed Mar 2 12:47:13 2016~~		-> Wed Aug 18 11:09:03 2021
			-> doMcall=0
	--------------		--------------
	abcSaf.cpp:		abcSaf.cpp:
	-doSaf 0		-doSaf 0
	1: perform multisample GL estimation		1: perform multisample GL estimation
	2: use an inbreeding version		2: use an inbreeding version
	3: calculate genotype probabilities (use -doPost 3 instead)		3: calculate genotype probabilities (use -doPost 3 instead)
	4: Assume genotype posteriors as input (still beta)		4: Assume genotype posteriors as input (still beta)
	~~-doThetas 0 (calculate thetas)~~		-underFlowProtect 0
	-underFlowProtect 0		-anc (null) (ancestral fasta)
	~~-fold 0 (deprecated)~~		-noTrans 0 (remove transitions)
	-anc (null) (ancestral fasta)		-pest (null) (prior SFS)
	-noTrans 0 (remove transitions)		-isHap 0 (is haploid beta!)
	-pest (null) (prior SFS)		-doPost 0 (doPost 3,used for accesing saf based variables)
	-isHap 0 (is haploid beta!)
	-doPost 0 (doPost 3,used for accesing saf based variables)
	NB:		NB:
	If -pest is supplied in addition to -doSaf then the output will then be posterior probability of the sample allelefrequency for each site		If -pest is supplied in addition to -doSaf then the output will then be posterior probability of the sample allelefrequency for each site

	</pre>		</pre>

Thorfinn at 15:52, 25 October 2019

2019-10-25T15:52:00Z

← Older revision		Revision as of 17:52, 25 October 2019
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	Latest version can now do bootstrapping.		Latest version can now do bootstrapping. Folding should now be done in realSFS and not in the saf file generation.

	=Quick Start=		=Quick Start=
Line 135:		Line 135:

	=Folded spectra=		=Folded spectra=
	If you don't have the ancestral state, you can instead estimate the folded SFS. This is done by supplying the -anc with the reference genome and ~~also supply~~ -fold 1.		If you don't have the ancestral state, you can instead estimate the folded SFS. This is done by supplying the -anc with the reference genome and applying -fold 1 to realSFS.


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	<pre>		<pre>
	#first generate .saf file		#first generate .saf file
	./angsd -bam bam.filelist -doSaf 1 -out smallFolded -anc chimpHg19.fa -GL 2 ~~-fold 1~~		./angsd -bam bam.filelist -doSaf 1 -out smallFolded -anc chimpHg19.fa -GL 2
	#now try the EM optimization with 4 threads		#now try the EM optimization with 4 threads
	misc/realSFS smallFolded.saf.idx -maxIter 100 -P 4 >smallFolded.sfs		misc/realSFS smallFolded.saf.idx -maxIter 100 -P 4 >smallFolded.sfs
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	This can be found in the angsd/doc/formats.pdf		This can be found in the angsd/doc/formats.pdf

	* If the -fold 1 has been set, then the dimension is no longer 2*nInd+1 but nInd+1		* If the -fold 1 has been set, then the dimension is no longer 2*nInd+1 but nInd+1 (this is deprecated)
	* If the -pest parameter has been supplied the output is no longer likelihoods but log posterior site allele frequencies		* If the -pest parameter has been supplied the output is no longer likelihoods but log posterior site allele frequencies

Thorfinn: /* Folded spectra */

2016-03-24T07:17:22Z

Folded spectra

← Older revision		Revision as of 09:17, 24 March 2016
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	=Folded spectra=		=Folded spectra=
	If you don't have the ancestral state, you can instead estimate the folded SFS. This is done by supplying the -anc with the reference genome and also supply -fold 1.		If you don't have the ancestral state, you can instead estimate the folded SFS. This is done by supplying the -anc with the reference genome and also supply -fold 1.
	~~Then you should remember to change the second parameter to the realSFS function as the number of individuals instead of the number of chromosomes.~~

	The above example would then be		The above example would then be

Thorfinn: /* Brief Overview */

2016-03-02T11:47:46Z

Brief Overview

← Older revision		Revision as of 13:47, 2 March 2016
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	=Brief Overview=		=Brief Overview=
	<pre>		<pre>
	./angsd -doSaf		./angsd -doSaf
	-> angsd version: 0.~~569~~ build(~~Dec 17 2013~~ 12:40:00)		-> angsd version: 0.910-76-gad32889 (htslib: 1.3-32-gecdc348) build(Mar 2 2016 12:38:33)
	-> Analysis helpbox/synopsis information:		-> Analysis helpbox/synopsis information:
			-> Command:
			./angsd -doSaf -> Wed Mar 2 12:47:13 2016
	--------------		--------------
	~~angsd_realSFS~~.cpp:		abcSaf.cpp:
	-doSaf 0		-doSaf 0
	1: perform multisample GL estimation		1: perform multisample GL estimation
	2: use an inbreeding version		2: use an inbreeding version
	3: calculate genotype probabilities (~~beta~~)		3: calculate genotype probabilities (use -doPost 3 instead)
	4: Assume genotype posteriors as input (still beta)		4: Assume genotype posteriors as input (still beta)
	-doThetas 0 (calculate thetas)		-doThetas 0 (calculate thetas)
	-underFlowProtect 0		-underFlowProtect 0
	-fold 0 (deprecated)		-fold 0 (deprecated)
	-anc (null) (ancestral fasta)		-anc (null) (ancestral fasta)
	-noTrans 0 (remove transitions)		-noTrans 0 (remove transitions)
	-pest (null) (prior SFS)		-pest (null) (prior SFS)
			-isHap 0 (is haploid beta!)
			-doPost 0 (doPost 3,used for accesing saf based variables)
			NB:
			If -pest is supplied in addition to -doSaf then the output will then be posterior probability of the sample allelefrequency for each site

	</pre>		</pre>

Thorfinn: /* -doSaf 2 */

2016-02-05T15:43:27Z

-doSaf 2

← Older revision		Revision as of 17:43, 5 February 2016
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	barplot(trueWithF[-1],main='true sfs F=0.9')		barplot(trueWithF[-1],main='true sfs F=0.9')

	estWithF<-~~exp(~~scan("withF.sfs"))		estWithF<-scan("withF.sfs")
	estNoF<-~~exp(~~scan("noF.sfs"))		estNoF<-scan("noF.sfs")

Thorfinn: /* Folded spectra */

2016-02-05T15:43:00Z

Folded spectra

← Older revision		Revision as of 17:43, 5 February 2016
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	misc/realSFS smallFolded.saf.idx -maxIter 100 -P 4 >smallFolded.sfs		misc/realSFS smallFolded.saf.idx -maxIter 100 -P 4 >smallFolded.sfs
	#in R		#in R
	sfs<-~~exp(~~scan("smallFolded.sfs"))		sfs<-scan("smallFolded.sfs")
	barplot(sfs[-1])		barplot(sfs[-1])
	</pre>		</pre>

Thorfinn at 12:29, 20 November 2015

2015-11-20T12:29:45Z

← Older revision		Revision as of 14:29, 20 November 2015
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	Latest version ~~on github,~~ can now do bootstrapping.		Latest version can now do bootstrapping.

	=Quick Start=		=Quick Start=

Thorfinn: /* How to plot */

2015-11-20T12:29:29Z

How to plot

@@ Line 153: / Line 153: @@
 * If the -fold 1 has been set, then the dimension is no longer 2*nInd+1 but nInd+1
 * If the -pest parameter has been supplied the output is no longer likelihoods but log posterior site allele frequencies
 =How to plot=