Main Page - Revision history

Emil: /* fastNGSAdmix */

2019-03-23T05:13:41Z

fastNGSAdmix

← Older revision		Revision as of 07:13, 23 March 2019
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	Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.		Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.

	= [[~~fastNGSAdmix~~]] =		= [[fastNGSadmix]] =

	Program for estimating admixture proportions and doing principal component analysis of a single NGS sample.		Program for estimating admixture proportions and doing principal component analysis of a single NGS sample.

Emil at 05:12, 23 March 2019

2019-03-23T05:12:17Z

← Older revision		Revision as of 07:12, 23 March 2019
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	Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.		Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.

			= [[fastNGSAdmix]] =

			Program for estimating admixture proportions and doing principal component analysis of a single NGS sample.

			= [[asaMap]] =

			Program for doing ancestry-specific association mapping in admixed populations, working with genotypes.

	= [[NgsRelate]] =		= [[NgsRelate]] =

Albrecht at 16:23, 4 December 2018

2018-12-04T16:23:19Z

← Older revision		Revision as of 18:23, 4 December 2018
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	R package for power estimation for a two-stage genome-wide association design. This is a modification of the code from Skol et al 2006, nat genet. so that the relative risk, case-control ratios and allele frequencies are allowed to vary between stages.		R package for power estimation for a two-stage genome-wide association design. This is a modification of the code from Skol et al 2006, nat genet. so that the relative risk, case-control ratios and allele frequencies are allowed to vary between stages.

			= [[IBSrelate]] =
	= [[LDadmix]] =		= [[LDadmix]] =
	= [[R scripts]] =		= [[R scripts]] =

Thorfinn at 12:39, 3 October 2018

2018-10-03T12:39:45Z

← Older revision		Revision as of 14:39, 3 October 2018
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	Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.		Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.


	~~= [[NgsRelate] ggg] =~~
	~~A software package for inferring relatedness and inbreeding between pairs of individuals from NGS data.~~

	= [[NgsRelate]] =		= [[NgsRelate]] =
	A software package for inferring relatedness and inbreeding between pairs of individuals from NGS data.		A software package for inferring relatedness and inbreeding between pairs of individuals from NGS data. This is a new version.

	= [[Relate]]=		= [[Relate]]=

Thorfinn: /* fastNGSadmix */

2018-10-03T12:38:23Z

fastNGSadmix

← Older revision		Revision as of 14:38, 3 October 2018
Line 20:		Line 20:
	A software package for inferring relatedness and inbreeding between pairs of individuals from NGS data.		A software package for inferring relatedness and inbreeding between pairs of individuals from NGS data.

	= [[~~fastNGSadmix~~]] =		= [[NgsRelate]] =
	Infers the ancestry proportions from NGS data of a single indivudal, even with low-depth NGS data. It is based on ngsAdmix, however it uses a referenece panel of population specific frequencies, and works when you have uncertainty in your data. This makes it ideal for ~~quick~~ and ~~easy analyses~~ of ~~medium and low depth sequencing~~ data samples where many genotypes cannot be called without introducing errors or ascertainment bias. There is also a PCA method for doing PCA of a NGS sample, where population structure is taken into into account.		A software package for inferring relatedness and inbreeding between pairs of individuals from NGS data.

	= [[Relate]]=		= [[Relate]]=

Thorfinn: /* NgsRelate */

2018-10-03T12:36:55Z

NgsRelate

← Older revision		Revision as of 14:36, 3 October 2018
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	= [[NgsRelate]] =		= [[NgsRelate] ggg] =
	A software package for inferring relatedness between pairs of individuals from NGS data.		A software package for inferring relatedness and inbreeding between pairs of individuals from NGS data.


	= [[fastNGSadmix]] =		= [[fastNGSadmix]] =

Thorfinn at 12:36, 3 October 2018

2018-10-03T12:36:16Z

← Older revision		Revision as of 14:36, 3 October 2018
Line 15:		Line 15:
	[[File:NgsAdmix.png\|thumb\|NGSadmix]]		[[File:NgsAdmix.png\|thumb\|NGSadmix]]
	Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.		Infer the ancestry proportions from low depth NGS data. The principal is the same as other softwares such as FRAPPE and ADMIXTURE however, ngsAdmix also works when you have uncertainty in your data. This makes it ideal for medium and low depth sequencing data where many genotypes cannot be called without introducing errors or ascertainment bias.


			= [[NgsRelate]] =
			A software package for inferring relatedness between pairs of individuals from NGS data.


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	= [[RelateAdmix]] =		= [[RelateAdmix]] =
	A software package for inferring relatedness between pairs of individuals even if the individuals are admixed.		A software package for inferring relatedness between pairs of individuals even if the individuals are admixed.

	~~= [[NgsRelate]] =~~
	~~A software package for inferring relatedness between pairs of individuals from NGS data.~~

	= [[BAMSE]] =		= [[BAMSE]] =

Emil: /* fastNGSadmix */

2017-03-05T15:06:06Z

fastNGSadmix

← Older revision		Revision as of 17:06, 5 March 2017
Line 18:		Line 18:

	= [[fastNGSadmix]] =		= [[fastNGSadmix]] =
	Infers the ancestry proportions from NGS data of a single indivudal, even with low-depth NGS data. It is based on ngsAdmix, however it uses a referenece panel of population specific frequencies, and works when you have uncertainty in your data. This makes it ideal for quick and easy analyses of medium and low depth sequencing data samples where many genotypes cannot be called without introducing errors or ascertainment bias. There is also a PCA method for doing PCA of a NGS sample, ~~also taking~~ population structure into account.		Infers the ancestry proportions from NGS data of a single indivudal, even with low-depth NGS data. It is based on ngsAdmix, however it uses a referenece panel of population specific frequencies, and works when you have uncertainty in your data. This makes it ideal for quick and easy analyses of medium and low depth sequencing data samples where many genotypes cannot be called without introducing errors or ascertainment bias. There is also a PCA method for doing PCA of a NGS sample, where population structure is taken into into account.

	= [[Relate]]=		= [[Relate]]=

Emil: /* fastNGSadmix */

2017-03-05T15:05:21Z

fastNGSadmix

← Older revision		Revision as of 17:05, 5 March 2017
Line 18:		Line 18:

	= [[fastNGSadmix]] =		= [[fastNGSadmix]] =
	~~Infer~~ the ancestry proportions from ~~low depth~~ NGS data of a single indivudal. ~~The principal~~ is ~~the same as~~ ngsAdmix, uses a referenece panel of population specific frequencies, ~~also~~ works when you have uncertainty in your data. This makes it ideal for quick and easy analyses of medium and low depth sequencing data samples where many genotypes cannot be called without introducing errors or ascertainment bias. ~~Also~~ a PCA method for taking population structure into account.		Infers the ancestry proportions from NGS data of a single indivudal, even with low-depth NGS data. It is based on ngsAdmix, however it uses a referenece panel of population specific frequencies, and works when you have uncertainty in your data. This makes it ideal for quick and easy analyses of medium and low depth sequencing data samples where many genotypes cannot be called without introducing errors or ascertainment bias. There is also a PCA method for doing PCA of a NGS sample, also taking population structure into account.

	= [[Relate]]=		= [[Relate]]=

Emil: /* fastNGSadmix */

2017-02-21T15:14:46Z

fastNGSadmix

← Older revision		Revision as of 17:14, 21 February 2017
Line 18:		Line 18:

	= [[fastNGSadmix]] =		= [[fastNGSadmix]] =
	~~[[thumb\|fastNGSadmix]]~~
	Infer the ancestry proportions from low depth NGS data of a single indivudal. The principal is the same as ngsAdmix, uses a referenece panel of population specific frequencies, also works when you have uncertainty in your data. This makes it ideal for quick and easy analyses of medium and low depth sequencing data samples where many genotypes cannot be called without introducing errors or ascertainment bias. Also a PCA method for taking population structure into account.		Infer the ancestry proportions from low depth NGS data of a single indivudal. The principal is the same as ngsAdmix, uses a referenece panel of population specific frequencies, also works when you have uncertainty in your data. This makes it ideal for quick and easy analyses of medium and low depth sequencing data samples where many genotypes cannot be called without introducing errors or ascertainment bias. Also a PCA method for taking population structure into account.