NgsAdmix - Revision history

Albrecht: Replaced content with "NGSadmix is a tool for estimating individual admixture proportions low depth sequencing data based on genotype likelihoods The software including tutorials can be found here https://github.com/aalbrechtsen/NGSadmix"

2026-03-24T07:28:40Z

Replaced content with "NGSadmix is a tool for estimating individual admixture proportions low depth sequencing data based on genotype likelihoods The software including tutorials can be found here https://github.com/aalbrechtsen/NGSadmix"

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Sonia4: /* Parameters */

2019-07-23T13:09:07Z

Parameters

← Older revision		Revision as of 15:09, 23 July 2019
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	For example, to get additional information, you would write '''-printInfo 1'''.		For example, to get additional information, you would write '''-printInfo 1'''.

	<~~code~~>./NGSadmix </~~code~~>		<pre>./NGSadmix </pre>

	Arguments:		Arguments:

Sonia4: /* Parameters */

2019-07-23T13:08:49Z

Parameters

← Older revision		Revision as of 15:08, 23 July 2019
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	For example, to get additional information, you would write '''-printInfo 1'''.		For example, to get additional information, you would write '''-printInfo 1'''.

	<~~pre~~>./NGSadmix </~~pre~~>		<code>./NGSadmix </code>

	Arguments:		Arguments:

Albrecht at 07:57, 12 July 2019

2019-07-12T07:57:13Z

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 The method was published in 2013 and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093]
 ==Download and Installation==
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 :NGSadmix is part of the package ANGSD. To install ANGSD, please follow the instructions here [http://popgen.dk/angsd/index.php/Installation]
 ==Quick start==

Albrecht: /* Installation */

2019-07-12T07:53:41Z

Installation

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	:* v31 june 24-2013; First public version.		:* v31 june 24-2013; First public version.

	==Installation==		==Download and Installation==

	NGSadmix can be installed independently or as a part of ANGSD.		NGSadmix can be installed independently or as a part of ANGSD.

Albrecht at 07:52, 12 July 2019

2019-07-12T07:52:28Z

← Older revision		Revision as of 09:52, 12 July 2019
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	~~This page contains information about the program called~~ NGSadmix~~, which~~ is a ~~very nice~~ tool for estimating individual admixture proportions from NGS data. It is based on genotype likelihoods and works well for medium and low coverage NGS data.		NGSadmix is a tool for estimating individual admixture proportions from NGS data. It is based on genotype likelihoods and works well for medium and low coverage NGS data.
	It is a fancy multithreaded c/c++ program which makes it useful for large datasets.		It is a fancy multithreaded c/c++ program which makes it useful for large datasets.

	The ~~great thing about~~ NGSadmix is that it ~~is a new method that~~ takes the uncertainty introduced in NGS sequencing data into account when inferring an individual's ancestry by using genotype likelihoods that considers the uncertainty caused by unobserved genotypes.		The strengths of NGSadmix is that it takes the uncertainty introduced in NGS sequencing data into account when inferring an individual's ancestry by using genotype likelihoods that considers the uncertainty caused by unobserved genotypes.

			As with the other existing software, ADMIXTURE and STRUCTURE, NGSadmix can detect admixture recent enough to cause structure in the population in terms of differing allele frequencies. Historical admixture events after which many generations has passed in the population, leaves no signature in terms of systematic differences in allele frequencies between individuals.

	As with the other existing software, ADMIXTURE and STRUCTURE, NGSadmix is only sensitive to admixture recent enough to cause structures in the population in terms of differing allele frequencies. Historical admixture events after which many generations has passed in the population, leaves no signature in terms of systematic differences in allele frequencies between individuals and are not a concern in association studies.

	[[File:NgsAdmix.png\|thumb]]		[[File:NgsAdmix.png\|thumb]]

	The method was published in 2013 and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093]		The method was published in 2013 and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093]


	==Software Download==		==Software Download==

Albrecht at 07:50, 12 July 2019

2019-07-12T07:50:11Z

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Albrecht: /* Allele frequency ouput (.fopt) */

2018-10-01T13:06:26Z

Allele frequency ouput (.fopt)

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	</pre>		</pre>
	</div>		</div>
	Use the -printInfo option to get the position of the lines in the fopt file if some sites have been flltered from the analysis (-minMaf, minInd, minLRT etc)		Use the "-printInfo 1" option to get the position of the lines in the fopt file if some sites have been flltered from the analysis (-minMaf, minInd, minLRT etc)

	==Admixture proportion output file (.qopt)==		==Admixture proportion output file (.qopt)==

Albrecht at 18:33, 9 November 2016

2016-11-09T18:33:28Z

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	[[File:NgsAdmix.png\|thumb]]		[[File:NgsAdmix.png\|thumb]]
	Latest version is 32 from June 25 2013. It can be found [http://popgen.dk/software/NGSadmix/ngsadmix32.cpp ]. Older versions can be found here:		Latest version is 32 from June 25 2013. It can be found [http://popgen.dk/software/download/NGSadmix/ngsadmix32.cpp ]. Older versions can be found here:
	[http://popgen.dk/software/NGSadmix/].		[http://popgen.dk/software/download/NGSadmix/].

	Method is published and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093]		Method is published and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093]
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	<pre>		<pre>
	wget popgen.dk/software/NGSadmix/ngsadmix32.cpp		wget popgen.dk/software/download/NGSadmix/ngsadmix32.cpp
	g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix		g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix
	</pre>		</pre>
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	First download some example test files which has been generated on basis of data from the 1000 genomes project (100 individuals from 5 populations with 50000 SNPs).		First download some example test files which has been generated on basis of data from the 1000 genomes project (100 individuals from 5 populations with 50000 SNPs).
	<pre>		<pre>
	wget popgen.dk/software/NGSadmix/data/input.gz		wget popgen.dk/software/download/NGSadmix/data/input.gz
	wget popgen.dk/software/NGSadmix/data/pop.info		wget popgen.dk/software/download/NGSadmix/data/pop.info
	</pre>		</pre>

Albrecht at 15:20, 4 January 2016

2016-01-04T15:20:18Z

← Older revision		Revision as of 17:20, 4 January 2016
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	=Brief Overview=		=Brief Overview=
			<div class="toccolours mw-collapsible mw-collapsed">
	<~~pre~~>
	./NGSadmix		./NGSadmix
			<pre class="mw-collapsible-content">
	Arguments:		Arguments:
	-likes Beagle likelihood filename		-likes Beagle likelihood filename
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	-minInd Minumum number of informative individuals		-minInd Minumum number of informative individuals
	</pre>		</pre>
			</div>
	NB All parameters are set using '''-par value'''. So to get additional information you would write '''-printInfo 1'''.		NB All parameters are set using '''-par value'''. So to get additional information you would write '''-printInfo 1'''.