FastNgsAdmixOld - Revision history

Albrecht: Albrecht moved page FastNgsAdmix to FastNgsAdmixOld without leaving a redirect: obsolute

2017-05-03T15:27:45Z

Albrecht moved page FastNgsAdmix to FastNgsAdmixOld without leaving a redirect: obsolute

← Older revision	Revision as of 17:27, 3 May 2017
(No difference)

Emil at 18:02, 19 February 2017

2017-02-19T18:02:10Z

← Older revision		Revision as of 20:02, 19 February 2017
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	<pre>		<pre>
	Rscript plinkToRef.R data/humanOrigins_7worldPops		Rscript R/plinkToRef.R data/humanOrigins_7worldPops
	</pre>		</pre>

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	<pre>		<pre>
	Rscript plinkToRef.R data/humanOrigins_7worldPops 0.05		Rscript R/plinkToRef.R data/humanOrigins_7worldPops 0.05
	</pre>		</pre>

Emil at 18:00, 19 February 2017

2017-02-19T18:00:49Z

← Older revision		Revision as of 20:00, 19 February 2017
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	The example below show how to make a beagle file of genotype likelihood using ANGSD.		The example below show how to make a beagle file of genotype likelihood using ANGSD.
	<pre>		<pre>
	HOME$ ./angsd -i ~~'pathtoindi~~.bam' -GL 2 -sites ~~'SNP~~.sites' -doGlf 2 -doMajorMinor 3 -minMapQ 30 -minQ 20 -doDepth 1 -doCounts 1 -out ~~indi_genotypelikelihood~~		HOME$ ./angsd -i example/smallNA12874.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.bam -GL 2 -sites data/humanOrigins_7worldPops.sites -doGlf 2 -doMajorMinor 3 -minMapQ 30 -minQ 20 -doDepth 1 -doCounts 1 -out example/smallNA12874.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.bam
	</pre>		</pre>

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	<pre>		<pre>
	Rscript plinkToRef.R ~~plinkFile~~		Rscript plinkToRef.R data/humanOrigins_7worldPops
	</pre>		</pre>

	This generates 3 files, a reference panel named refPanel_plinkFile.txt, a number of individuals file called nInd_plinkFile.txt and a plinkFile.sites file with chr pos and minor major alleles.		This generates 3 files, a reference panel named refPanel_plinkFile.txt, a number of individuals file called nInd_plinkFile.txt and a plinkFile.sites file with chr pos and minor major alleles.
	The .fam file must have the group or population specified as FID, meaning first column and then the individual ID as the second column:		The .fam file must have the group or population specified as FID, meaning first column and then the individual ID as the second column:


	<pre>		<pre>
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	<pre>		<pre>
	Rscript plinkToRef.R ~~plinkFile~~ 0.05		Rscript plinkToRef.R data/humanOrigins_7worldPops 0.05
	</pre>		</pre>

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	<pre>		<pre>
	./fastNGSadmix -likes ~~indi_genotypelikelihood~~.beagle -fname ~~refPanel~~.txt -Nname ~~nInd~~.txt -outfiles ~~indi_genotypelikelihood.beagle~~ -K 3		./fastNGSadmix -likes NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz -fname data/refPanel_humanOrigins_7worldPops.txt -Nname data/nInd_humanOrigins_7worldPops.txt -outfiles NA12763_CEU -K 3
	</pre>		</pre>

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	It should also be noted that the program quits if there are duplicate sites (based on chr_pos ID) in the input or the reference panel.		It should also be noted that the program quits if there are duplicate sites (based on chr_pos ID) in the input or the reference panel.

	It then produces two files ~~indi_genotypelikelihood.beagle~~.qopt with the admixture proportions and ~~indi_genotypelikelihood.beagle~~.log.		It then produces two files NA12763_CEU.qopt with the admixture proportions and NA12763_CEU.log.

	Or with a plink file:		Or with a plink file (no provided example plink file):

	<pre>		<pre>
	./fastNGSadmix -plink plinkFile -fname ~~refPanel~~.txt -Nname ~~nInd~~.txt -outfiles plinkFile -K 3		./fastNGSadmix -plink plinkFile -fname data/refPanel_humanOrigins_7worldPops.txt -Nname data/nInd_humanOrigins_7worldPops.txt -outfiles plinkFile -K 3
	</pre>		</pre>

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	By default the method adjusting the frequencies is used, to use the unadjusted approach set "-doAdjust 0". The accelerated EM algorithm is used by default, to use regular EM algorithm set "-method 0".		By default the method adjusting the frequencies is used, to use the unadjusted approach set "-doAdjust 0". The accelerated EM algorithm is used by default, to use regular EM algorithm set "-method 0".

	~~OPTIONS OPTIONS OPTIONS!??~~

	'''PCA'''		'''PCA'''
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	<pre>		<pre>
	Rscript fastNGSAdmixPCA.R likes=~~indi_genotypelikelihood~~.beagle qopt=~~indi_genotypelikelihood~~.beagle.qopt out=~~indi_genotypelikelihood.beagle~~ geno=~~refPanel~~		Rscript R/fastNGSAdmixPCA.R likes=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz qopt=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz.qopt out=NA12763_CEU geno=data/humanOrigins_7worldPops
	</pre>		</pre>

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	<pre>		<pre>
	Rscript fastNGSAdmixPCA.R plinkFile=plinkFile qopt=plinkFile.qopt out=plinkFile geno=~~refPanel~~		Rscript R/fastNGSAdmixPCA.R plinkFile=plinkFile qopt=plinkFile.qopt out=plinkFile geno=data/humanOrigins_7worldPops
	</pre>		</pre>

Emil at 15:45, 18 February 2017

2017-02-18T15:45:39Z

← Older revision		Revision as of 17:45, 18 February 2017
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	Rscript fastNGSAdmixPCA.R likes=indi_genotypelikelihood.beagle qopt=indi_genotypelikelihood.beagle.qopt out=indi_genotypelikelihood.beagle geno=refPanel		Rscript fastNGSAdmixPCA.R likes=indi_genotypelikelihood.beagle qopt=indi_genotypelikelihood.beagle.qopt out=indi_genotypelikelihood.beagle geno=refPanel
	</pre>		</pre>


	Or using analyzed plink files.		Or using analyzed plink files.
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	By default the populations of the analyzed *.qopt file are used. It can be specified which PCs should be plotted (default PC1 and PC2), by for example giving PCs=2,3 as an argument (if PC2 and PC3).		By default the populations of the analyzed *.qopt file are used. It can be specified which PCs should be plotted (default PC1 and PC2), by for example giving PCs=2,3 as an argument (if PC2 and PC3).
			The script also generates barplots of the admixture proportions supplied with confidence intervals.

	The '''snpStats''' R package, is needed for running this script.		The '''snpStats''' R package, is needed for running this script.

Emil at 14:34, 18 February 2017

2017-02-18T14:34:40Z

← Older revision		Revision as of 16:34, 18 February 2017
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	The '''snpStats''' R package, is needed for running this script.		The '''snpStats''' R package, is needed for running this script.










	~~Custom refpanel can be supplied, has to look like this, where the 5 first columns have to be, then populations frequencies:~~

	~~chr,pos,name,A0,A1~~

	~~The frequencies have to be of the A0 allele.~~

	~~Basically the files have to look like this:~~
	~~bgl rs1 A B GL(AA) GL(AB) GL(BB) Then ref 1 1 rs1 B A f(B)~~

	~~Then solution is this:~~
	~~bgl rs1 A B GL(AA) GL(AB) GL(BB) Then ref 1 1 rs1 B A 1-f(B)~~

	~~Then prepFreqs.R will take care of preparing the files properly.~~

	~~Example of running prepFreqs.R:~~

	~~<pre>~~
	~~Rscript prepFreqs.R indi_genotypelikelihood.bgl~~
	~~</pre>~~

	~~Can also specify other populations than the default 5 ones in the reference panel. Also a custom made reference panel can be supplied (has to be .Rdata file).~~

	~~<pre>~~
	~~Rscript prepFreqs.R indi_genotypelikelihood.bgl Pop1,Pop2,Pop3,Pop4 customRefPanel~~
	~~</pre>~~


	~~indi_genotypelikelihood~~

	~~Then run prepFreqs.R to get the proper beagle, refpanel and nInd files for the analysis.~~

	~~Then run fastNGSadmix.~~

	~~All the awesome options with the program.~~


	~~So bgl~~
	~~rs1 A B GL(AA) GL(AB) GL(BB)~~
	~~Then ref~~
	~~1 1 rs1 A B f(A)~~

	~~(So if the 3 columns with genotype likelihoods in the beagle file is coded like this AA AB BB, then the frequencies should be of the A allele.)~~

	~~Furthermore a file with the number of individuals in each reference population should be supplied.~~



	~~Then a lot of different options and filters can be specified:~~

	~~(TO BE CONTINUED...)~~

Emil at 14:34, 18 February 2017

2017-02-18T14:34:11Z

@@ Line 1: / Line 1: @@
 This page contains information about the program called fastNGSadmix which is a very fast tool for finding admixture proportions from NGS data of a single individual and a method for doing PCA of NGS data, using the estimated admixture proporitions. It is based on genotype likelihoods. The admixture estimation part is written in C++ and the PCA part is written in R.
 =Installation=
-wget http://popgen.dk/albrecht/kristian/tool_download.zip
+The program + more can be downloaded from:
-AND THEN CLONE FROM GITHUB FOR C++ PROGRAM
+https://github.com/e-jorsboe/fastNGSadmix
 =Input Files=

Emil at 20:21, 10 February 2017

2017-02-10T20:21:55Z

← Older revision		Revision as of 22:21, 10 February 2017
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	</pre>		</pre>

	By default the populations of the analyzed *.qopt file are used. It can be specified which PCs should be plotted (default PC1 and PC2).		By default the populations of the analyzed *.qopt file are used. It can be specified which PCs should be plotted (default PC1 and PC2), by for example giving PCs=2,3 as an argument (if PC2 and PC3).

	The '''snpStats''' R package, is needed for running this script.		The '''snpStats''' R package, is needed for running this script.

Emil at 20:14, 10 February 2017

2017-02-10T20:14:49Z

← Older revision		Revision as of 22:14, 10 February 2017
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	The example below show how to make a beagle file of genotype likelihood using ANGSD.		The example below show how to make a beagle file of genotype likelihood using ANGSD.
	<pre>		<pre>
	HOME$ .~~/angsd0.594~~/angsd -i 'pathtoindi.bam' -GL 2 -sites 'SNP.sites' -doGlf 2 -doMajorMinor 3 -minMapQ 30 -minQ 20 -doDepth 1 -doCounts 1 -out indi_genotypelikelihood		HOME$ ./angsd -i 'pathtoindi.bam' -GL 2 -sites 'SNP.sites' -doGlf 2 -doMajorMinor 3 -minMapQ 30 -minQ 20 -doDepth 1 -doCounts 1 -out indi_genotypelikelihood
	</pre>		</pre>

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	(refPanel is the binary plink files, refPanel.bim, refPanel.fam and refPanel.bed)		(refPanel is the binary plink files, refPanel.bim, refPanel.fam and refPanel.bed)

	Rscript fastNGSAdmixPCA.R ~~GLfile~~=indi_genotypelikelihood.beagle ~~admixFile~~=indi_genotypelikelihood.beagle.qopt out=indi_genotypelikelihood.beagle ~~genoFile~~=refPanel		<pre>
			Rscript fastNGSAdmixPCA.R likes=indi_genotypelikelihood.beagle qopt=indi_genotypelikelihood.beagle.qopt out=indi_genotypelikelihood.beagle geno=refPanel
			</pre>


	Or using analyzed plink files.		Or using analyzed plink files.

	Rscript fastNGSAdmixPCA.R plinkFile=plinkFile ~~admixFile~~=plinkFile.qopt out=plinkFile ~~genoFile~~=refPanel		<pre>
			Rscript fastNGSAdmixPCA.R plinkFile=plinkFile qopt=plinkFile.qopt out=plinkFile geno=refPanel
			</pre>

	By default the populations of the analyzed *.qopt file are used. It can be specified which PCs should be plotted (default PC1 and PC2).		By default the populations of the analyzed *.qopt file are used. It can be specified which PCs should be plotted (default PC1 and PC2).

	The snpStats R package, is needed for running this script.		The '''snpStats''' R package, is needed for running this script.



	~~#########~~
	~~### PCA part~~
	~~########~~

Emil at 14:35, 9 February 2017

2017-02-09T14:35:35Z

← Older revision		Revision as of 16:35, 9 February 2017
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	The .fam file must have the group or population specified as FID, meaning first column and then the individual ID as the second column:		The .fam file must have the group or population specified as FID, meaning first column and then the individual ID as the second column:


			<pre>
	French F1 0 0 1 1		French F1 0 0 1 1
	French F2 0 0 1 1		French F2 0 0 1 1
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	Yoruba Y3 0 0 2 1		Yoruba Y3 0 0 2 1
	...		...
			</pre>

	A second argument of MAF threshold can be supplied, meaning all sites where the MAF is below this in any population is removed.		A second argument of MAF threshold can be supplied, meaning all sites where the MAF is below this in any population is removed.
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	</pre>		</pre>

	The snpStats R package, is needed for running the plinkToRef.R script.		The '''snpStats R package''', is needed for running the plinkToRef.R script.



	fastNGSadmix already comes with a premade reference panel, made from Lazaridis et al. (2014) where the curated dataset was selected.		fastNGSadmix already comes with a premade reference panel, made from Lazaridis et al. (2014) where the curated dataset was selected.
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	I lifted the dataset hg19 using the program liftOver, I then translated snpNames to rs names, using 1000G data, generating a unique name for each site via "chr-pos-A1-A2" (where A1 and A2 are alphabetically sorted).		I lifted the dataset hg19 using the program liftOver, I then translated snpNames to rs names, using 1000G data, generating a unique name for each site via "chr-pos-A1-A2" (where A1 and A2 are alphabetically sorted).

	Furthermore I removed sites with more than 5 % missing and a MAF below 5 %, and only autosomal sites.		Furthermore I removed sites with more than 5 % missing and a MAF below 5 %, and kept only autosomal sites.
	I selected 5 populations French, Han, Karitiana, Papuan and Yoruba to have representation for most of the world.		I selected 7 populations French, Han, Chukchi, Karitiana, Papuan, Sindhi and Yoruba to have representation for most of the world.
	Furthermore I made sure that I only used unadmixed individuals within each population.		Furthermore I made sure that I only used unadmixed individuals within each population.

Emil at 14:32, 9 February 2017

2017-02-09T14:32:21Z

← Older revision		Revision as of 16:32, 9 February 2017
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	</pre>		</pre>

			AND THEN CLONE FROM GITHUB FOR C++ PROGRAM


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	A provided SNP.sites file has been included.		A provided SNP.sites file has been included.

	~~</pre>~~		The program needs a reference panel of population specific frequencies, populations for which admixture proportions should be estimated,


	The program ~~also~~ needs ~~frequencies of~~ a reference panel ~~with the~~ populations for which admixture proportions should be estimated,
	for instance from 1000 G or HGDP, or another custom made reference panel. The program also needs a file telling the size of each reference panel population.		for instance from 1000 G or HGDP, or another custom made reference panel. The program also needs a file telling the size of each reference panel population.
	There is an R script ~~called plinkToRefV2~~.R, that can convert a plink file to a reference panel and size of reference panel populations.		There is an R script plinkToRef.R, that can convert a plink file to a reference panel and size of reference panel populations.
	Example:		Example: