Fst PCA - Revision history

Thorfinn at 14:21, 30 July 2015

2015-07-30T14:21:35Z

← Older revision		Revision as of 16:21, 30 July 2015
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	https://github.com/mfumagalli/ngsTools		https://github.com/mfumagalli/ngsTools

			=Fst=
	~~=Old nice version=~~
	==Fst==
	# Generate .saf files from each population using ANGSD [[SFS Estimation]]		# Generate .saf files from each population using ANGSD [[SFS Estimation]]
	## using a 2D-SFS as a prior, estimated using ngs2dSFS		## using a 2D-SFS as a prior, estimated using ngs2dSFS
	## using marginal spectra as priors, estimated using '''realSFS'''		## using marginal spectra as priors, estimated using '''realSFS'''

	==PCA==		=PCA=
	More information here:		More information here:
	https://github.com/mfumagalli/ngsTools#ngscovar		https://github.com/mfumagalli/ngsTools#ngscovar

Thorfinn at 14:21, 30 July 2015

2015-07-30T14:21:09Z

← Older revision		Revision as of 16:21, 30 July 2015
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			;THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions
	Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files.		Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files.

Thorfinn at 14:20, 30 July 2015

2015-07-30T14:20:19Z

Show changes

Thorfinn at 13:56, 30 July 2015

2015-07-30T13:56:11Z

← Older revision		Revision as of 15:56, 30 July 2015
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	We are also working on a new implementation that generalizes the above approach to multiple populations.		We are also working on a new implementation that generalizes the above approach to multiple populations.

			Our program can estimate fst between two populations. And has been generalized to give all pairwise fst estimates if you supply the command with multiple populations.

			;if you supply 3 populations, the program will also output the pbs statistic.

	=New Fancy Version=		=New Fancy Version=

Thorfinn: /* Sliding Window output */

2015-07-30T13:51:39Z

Sliding Window output

← Older revision		Revision as of 15:51, 30 July 2015
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	;fst.unweight(pop1,pop2) fst.weight(pop1,pop2) fst.unweight(pop1,pop3) fst.weight(pop1,pop3) fst.unweight(pop2,pop3) fst.weight(pop2,pop3)		;fst.unweight(pop1,pop2) fst.weight(pop1,pop2) fst.unweight(pop1,pop3) fst.weight(pop1,pop3) fst.unweight(pop2,pop3) fst.weight(pop2,pop3)
	<pre>		<pre>
	(~~9134~~,~~58932~~)(14010000,~~14060000~~)(14010000,14060000) 1 14035000 0.~~017180~~ 0.~~020672~~ 0.~~024635~~ 0.~~014321~~ 0.~~025134~~ 0.~~035149~~		(9133,58895)(14010000,14059999)(14010000,14060000) 1 14035000 0.022099 0.016387 0.026686 0.027731 0.025311 0.047920 -0.002231 0.035045 0.030353
	(~~19115~~,~~68918~~)(14020000,~~14070000~~)(14020000,14070000) 1 14045000 0.~~017143~~ 0.~~023498~~ 0.~~024781~~ 0.~~015975~~ 0.~~025092~~ 0.~~039462~~		(19114,68881)(14020000,14069999)(14020000,14070000) 1 14045000 0.022096 0.019076 0.026777 0.024238 0.025290 0.052793 -0.005220 0.041969 0.029757
	(~~28987~~,~~78694~~)(14030000,~~14080000~~)(14030000,14080000) 1 14055000 0.~~017134~~ 0.~~026566~~ 0.~~024849~~ 0.~~017496~~ 0.~~025065~~ 0.~~041826~~		(28951,78655)(14030000,14079999)(14030000,14080000) 1 14055000 0.022043 0.021025 0.026915 0.023368 0.025342 0.056975 -0.006884 0.046840 0.030530
	(~~38964~~,~~88671~~)(14040000,~~14090000~~)(14040000,14090000) 1 14065000 0.~~017122~~ 0.~~018710~~ 0.~~024786~~ 0.~~021365~~ 0.~~025009~~ 0.~~040310~~		(38928,88632)(14040000,14089999)(14040000,14090000) 1 14065000 0.022083 0.016525 0.026846 0.029560 0.025345 0.053421 -0.004116 0.039898 0.034122
	(~~48953~~,~~98209~~)(14050000,~~14100000~~)(14050000,14100000) 1 14075000 0.~~017141~~ 0.~~021010~~ 0.~~024710~~ 0.~~020557~~ 0.~~024806~~ 0.~~028282~~		(48917,98170)(14050000,14099999)(14050000,14100000) 1 14075000 0.022132 0.022082 0.026742 0.025564 0.025262 0.037071 0.005226 0.024827 0.020671
	(75,~~49193~~)(14000000,~~14050000~~)(14000000,14050000) 10 14025000 0.~~017165~~ 0.~~074410~~ 0.~~024862~~ 0.~~118005~~ 0.~~025311~~ 0.~~003885~~		(74,49191)(14000000,14049999)(14000000,14050000) 10 14025000 0.022704 0.101955 0.026479 0.095713 0.025102 0.001924 0.103108 -0.048378 -0.002500
			(9734,58555)(14010000,14059999)(14010000,14060000) 10 14035000 0.022779 0.102670 0.026425 0.088015 0.025118 0.002721 0.098870 -0.043342 -0.006738
	</pre>		</pre>
			The last 3 columns are the populations branch statistic for population1, popultion2 and population3

	== 3 Populations simulated data==		== 3 Populations simulated data==

Thorfinn: /* 3 Populations real data */

2015-07-30T13:50:19Z

3 Populations real data

← Older revision		Revision as of 15:50, 30 July 2015
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	-> pbs.pop2 0.005088		-> pbs.pop2 0.005088
	-> pbs.pop3 0.009367		-> pbs.pop3 0.009367

	~~./misc/realSFS fst stats here.fst.idx~~
	~~-> FST.Unweight[nObs:1666316]:0.017247 Fst.Weight:0.031039~~
	~~-> FST.Unweight[nObs:1666316]:0.024852 Fst.Weight:0.029915~~
	~~-> FST.Unweight[nObs:1666316]:0.025416 Fst.Weight:0.019600~~
	#below is not tested that much, but seems to work		#below is not tested that much, but seems to work
	../misc/realSFS fst stats2 here.fst.idx -win 50000 -step 10000 >slidingwindow		../misc/realSFS fst stats2 here.fst.idx -win 50000 -step 10000 >slidingwindow

Thorfinn: /* 3 Populations real data */

2015-07-30T13:50:00Z

3 Populations real data

@@ Line 40: / Line 40: @@
 ./misc/realSFS fst index pop1.saf.idx pop2.saf.idx pop3.saf.idx -sfs pop1.pop2.ml -sfs pop1.pop3.ml -sfs pop2.pop3.ml -fstout here
 #get the global estimate
 ./misc/realSFS fst stats here.fst.idx
 	-> FST.Unweight[nObs:1666316]:0.017247 Fst.Weight:0.031039

Thorfinn: /* 3 Populations real data */

2015-07-30T13:48:47Z

3 Populations real data

← Older revision		Revision as of 15:48, 30 July 2015
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	==3 Populations real data==		==3 Populations real data==
	In commands below im using 24 threads, because this is what I have. Adjust ~~according ly~~		In commands below im using 24 threads, because this is what I have. Adjust accordingly
	<pre>		<pre>
	#this is with 2pops		#this is with 2pops
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	../misc/realSFS fst stats2 here.fst.idx -win 50000 -step 10000 >slidingwindow		../misc/realSFS fst stats2 here.fst.idx -win 50000 -step 10000 >slidingwindow
	</pre>		</pre>
			In the presence of 3 populations, the program will also calculate the population branch statistics
	===Sliding Window output===		===Sliding Window output===
	The sliding window seems to work so we have documented it here:		The sliding window seems to work so we have documented it here:

Thorfinn: /* 3 Populations real data */

2015-07-30T12:45:54Z

3 Populations real data

← Older revision		Revision as of 14:45, 30 July 2015
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	./misc/realSFS pop2.saf.idx pop3.saf.idx -P 24 >pop2.pop3.ml		./misc/realSFS pop2.saf.idx pop3.saf.idx -P 24 >pop2.pop3.ml
	#prepare the fst for easy analysis etc		#prepare the fst for easy analysis etc
	../misc/realSFS fst index pop1.saf.idx pop2.saf.idx pop3.saf.idx -sfs pop1.pop2.ml -sfs pop1.pop3.ml -sfs pop2.pop3.ml -fstout here		./misc/realSFS fst index pop1.saf.idx pop2.saf.idx pop3.saf.idx -sfs pop1.pop2.ml -sfs pop1.pop3.ml -sfs pop2.pop3.ml -fstout here
	#get the global estimate		#get the global estimate
	../misc/realSFS fst stats here.fst.idx		./misc/realSFS fst stats here.fst.idx
	-> FST.Unweight[nObs:1666316]:0.017247 Fst.Weight:0.031039		-> FST.Unweight[nObs:1666316]:0.017247 Fst.Weight:0.031039
	-> FST.Unweight[nObs:1666316]:0.024852 Fst.Weight:0.029915		-> FST.Unweight[nObs:1666316]:0.024852 Fst.Weight:0.029915

Thorfinn: /* 3 Populations real data */

2015-07-30T12:42:39Z

3 Populations real data

← Older revision		Revision as of 14:42, 30 July 2015
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	./angsd -b list12 -anc hg19ancNoChr.fa -out pop3 -dosaf 1 -gl 1		./angsd -b list12 -anc hg19ancNoChr.fa -out pop3 -dosaf 1 -gl 1
	#calculate all pairwise 2dsfs's		#calculate all pairwise 2dsfs's
	../misc/realSFS pop1.saf.idx pop2.saf.idx -P 24 >pop1.pop2.ml		./misc/realSFS pop1.saf.idx pop2.saf.idx -P 24 >pop1.pop2.ml
	../misc/realSFS pop1.saf.idx pop3.saf.idx -P 24 >pop1.pop3.ml		./misc/realSFS pop1.saf.idx pop3.saf.idx -P 24 >pop1.pop3.ml
	../misc/realSFS pop2.saf.idx pop3.saf.idx -P 24 >pop2.pop3.ml		./misc/realSFS pop2.saf.idx pop3.saf.idx -P 24 >pop2.pop3.ml
	#prepare the fst for easy analysis etc		#prepare the fst for easy analysis etc
	../misc/realSFS fst index pop1.saf.idx pop2.saf.idx pop3.saf.idx -sfs pop1.pop2.ml -sfs pop1.pop3.ml -sfs pop2.pop3.ml -fstout here		../misc/realSFS fst index pop1.saf.idx pop2.saf.idx pop3.saf.idx -sfs pop1.pop2.ml -sfs pop1.pop3.ml -sfs pop2.pop3.ml -fstout here