2d SFS Estimation - Revision history

Thorfinn at 01:26, 17 August 2019

2019-08-17T01:26:23Z

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	Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation\|method]]. Newer versions of ANGSD can estimate even higher dimensions (upto 4). From august17 2019 the program can now do a proper folding, which is done by supplying it with the UNFOLDED saf.idx fiels generated by -dosaf 1		Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation\|method]].
			* Newer versions of ANGSD can estimate even higher dimensions (upto 4).
			* From august17 2019 the program can now do a proper folding of the 2dsfs, which is done by supplying it with the UNFOLDED saf.idx fiels generated by -dosaf 1

	Below are some examples:		Below are some examples:


	And is best explained by a full example.		And is best explained by a full example.
	==Example==		==Example==

Thorfinn at 01:25, 17 August 2019

2019-08-17T01:25:47Z

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	</pre>		</pre>
	The output is then located in a nice flattened matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.		The output is then located in a nice flattened matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.

			==2d sfs (folded)==
			<pre>
			#2d sfs for pop1 and pop2 doing proper folding
			realSFS pop1.saf.idx pop2.saf.idx -P 24 -fold 1 >2dsfs.sfs
			</pre>

Thorfinn at 01:24, 17 August 2019

2019-08-17T01:24:37Z

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	</pre>		</pre>

			==1 dimensional frequency spectra==
	If we were interested in estimating the 1d sfs for each population we could do it like this using the [[realSFS]] program. (See more on [[SFS Estimation \|page]] )		If we were interested in estimating the 1d sfs for each population we could do it like this using the [[realSFS]] program. (See more on [[SFS Estimation \|page]] )
	<pre>		<pre>

Thorfinn at 01:23, 17 August 2019

2019-08-17T01:23:51Z

← Older revision		Revision as of 03:23, 17 August 2019
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	Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation\|method]]. ~~Never~~ versions of ANGSD can estimate even higher dimensions (upto 4)		Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation\|method]]. Newer versions of ANGSD can estimate even higher dimensions (upto 4). From august17 2019 the program can now do a proper folding, which is done by supplying it with the UNFOLDED saf.idx fiels generated by -dosaf 1

			Below are some examples:


	And is best explained by a full example.		And is best explained by a full example.
	=Example=		==Example==
	* Assume you have a 12 bamfiles for population in the file '''pop1.list'''		* Assume you have a 12 bamfiles for population in the file '''pop1.list'''
	* Assume you have a 14 bamfiles for population in the file '''pop2.list'''		* Assume you have a 14 bamfiles for population in the file '''pop2.list'''

Thorfinn: /* Example */

2015-05-11T12:39:30Z

Example

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	realSFS pop2.saf.idx -P 24 >pop2.saf.sfs		realSFS pop2.saf.idx -P 24 >pop2.saf.sfs
	#2d sfs for pop1 and pop2		#2d sfs for pop1 and pop2
	realSFS pop1.saf.idx pop2.saf.idx -P 24		realSFS pop1.saf.idx pop2.saf.idx -P 24 >2dsfs.sfs
	</pre>		</pre>
	The output is then located in a nice matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.		The output is then located in a nice flattened matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.

Thorfinn: /* Example */

2015-05-11T12:38:40Z

Example

← Older revision		Revision as of 14:38, 11 May 2015
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	realSFS pop2.saf.idx -P 24 >pop2.saf.sfs		realSFS pop2.saf.idx -P 24 >pop2.saf.sfs
	#2d sfs for pop1 and pop2		#2d sfs for pop1 and pop2
	~~#first argument is saf file, -P 24 is the number of cores we want to use~~
	realSFS pop1.saf.idx pop2.saf.idx -P 24		realSFS pop1.saf.idx pop2.saf.idx -P 24
	~~And we now estimate the joint site frequency spectra by using the [[realSFS]] program~~		</pre>
	<pre>
	The output is then located in a nice matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.		The output is then located in a nice matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.

Thorfinn: /* Example */

2015-05-11T12:38:17Z

Example

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	angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2 -doSaf 1		angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2 -doSaf 1
	</pre>		</pre>
	~~Each run will generate 2 files of interest: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos'''~~

	If we were interested in estimating the 1d sfs for each population we could do it like this using the [[realSFS]] program. (See more on [[SFS Estimation \|page]] )		If we were interested in estimating the 1d sfs for each population we could do it like this using the [[realSFS]] program. (See more on [[SFS Estimation \|page]] )

Thorfinn: /* Example */

2015-05-11T12:37:56Z

Example

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	* Assume you have a 14 bamfiles for population in the file '''pop2.list'''		* Assume you have a 14 bamfiles for population in the file '''pop2.list'''
	* Assume you have a fastafile containing the ancestral state in the '''anc.fa'''		* Assume you have a fastafile containing the ancestral state in the '''anc.fa'''
	* Assume we are only interested in '''chr1'''

	Let's start by finding the positions for which we have data in population1 and population2		Let's start by finding the positions for which we have data in population1 and population2
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	If we were interested in estimating the 1d sfs for each population we could do it like this using the [[realSFS]] program. (See more on [[SFS Estimation \|page]] )		If we were interested in estimating the 1d sfs for each population we could do it like this using the [[realSFS]] program. (See more on [[SFS Estimation \|page]] )
	<pre>		<pre>
	realSFS pop1.saf 24 -P 24 >pop1.saf.sfs		#sfs for pop1
	realSFS pop2.saf 28 -P 24 >pop2.saf.sfs		realSFS pop1.saf.idx -P 24 >pop1.saf.sfs
	#first argument is saf file, ~~second argument is the number of chromosomes,~~ -P 24 is the number of cores we want to use		#sfs for pop2
	~~</pre>~~		realSFS pop2.saf.idx -P 24 >pop2.saf.sfs
	~~Now we find the positions that occurs both in population1 and population2 using the '''uniq''' POSIX program.~~		#2d sfs for pop1 and pop2
	~~<pre>~~		#first argument is saf file, -P 24 is the number of cores we want to use
	~~gunzip -c~~ pop1.saf.~~pos.gz~~ pop2.saf.~~pos.gz\|sort -S 50%\|uniq -d\|sort -k1,1 -S 50% >intersect.txt~~		realSFS pop1.saf.idx pop2.saf.idx -P 24
	~~</pre>~~
	~~And now we redo the angsd sample allelefrequence calculation by conditioning on the sites that occur in both populations~~

	~~<pre>~~
	~~# as always you can add -minMapQ 1 and -minQ 20 to only keep high quality data.~~
	~~angsd -GL 1 -b pop1.list -anc anc.fa -r chr1:~~ -P ~~10 -out pop1 -sites intersect.txt -doSaf 1~~
	~~angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2 -sites intersect.txt -doSaf 1~~
	~~</pre>~~
	~~Notice that the last 2 commands will overwrite the: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos''' files.~~


	And we now estimate the joint site frequency spectra by using the [[realSFS]] program		And we now estimate the joint site frequency spectra by using the [[realSFS]] program
	<pre>		<pre>
	~~realSFS 2dsfs pop1.saf pop2.saf 24 28 -P 24 >2dsfs.sfs~~
	~~</pre>~~
	The output is then located in a nice matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.		The output is then located in a nice matrix format(25x29) in the file: '''2dsfs.sfs'''. Good luck visualising it, some people are using dadi, we have been using heat maps in R.

Thorfinn at 12:34, 11 May 2015

2015-05-11T12:34:12Z

← Older revision		Revision as of 14:34, 11 May 2015
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	Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation\|method]].		Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation\|method]]. Never versions of ANGSD can estimate even higher dimensions (upto 4)

	The method works by calculating population specific sample allele frequencies. A minor annoyance in the current implementation is that you will need to limit the analysis to the sites that has coverage in both populations. This in effect means that you will need to do two passes for each population.

	And is best explained by a full example.		And is best explained by a full example.

Thorfinn: /* Example */

2014-09-09T18:06:28Z

Example

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	<pre>		<pre>
	# as always you can add -minMapQ 1 and -minQ 20 to only keep high quality data.		# as always you can add -minMapQ 1 and -minQ 20 to only keep high quality data.
	angsd -GL 1 -b pop1.list -anc anc.fa -r chr1: -P 10 -out pop1		angsd -GL 1 -b pop1.list -anc anc.fa -r chr1: -P 10 -out pop1 -doSaf 1
	angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2		angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2 -doSaf 1
	</pre>		</pre>
	Each run will generate 2 files of interest: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos'''		Each run will generate 2 files of interest: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos'''
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	<pre>		<pre>
	# as always you can add -minMapQ 1 and -minQ 20 to only keep high quality data.		# as always you can add -minMapQ 1 and -minQ 20 to only keep high quality data.
	angsd -GL 1 -b pop1.list -anc anc.fa -r chr1: -P 10 -out pop1 -sites intersect.txt		angsd -GL 1 -b pop1.list -anc anc.fa -r chr1: -P 10 -out pop1 -sites intersect.txt -doSaf 1
	angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2 -sites intersect.txt		angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2 -sites intersect.txt -doSaf 1
	</pre>		</pre>
	Notice that the last 2 commands will overwrite the: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos''' files.		Notice that the last 2 commands will overwrite the: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos''' files.