HWE and Inbreeding estimates - Revision history

Albrecht: /* Site estimate of inbreeding coefficient (HWE test) */

2018-02-07T14:59:33Z

Site estimate of inbreeding coefficient (HWE test)

← Older revision		Revision as of 16:59, 7 February 2018
Line 3:		Line 3:
	;-HWE_pval_F		;-HWE_pval_F

	By choosing '''HWE_pval_F 1''', no sites will be filtered but the p-value along ~~wight~~ the frequency, and F for the sites will be dumped in '''.hweF.gz''' file.		By choosing '''HWE_pval_F 1''', no sites will be filtered but the p-value along with the frequency, and F for the sites will be dumped in '''.hweF.gz''' file.

	=Estimation of individual inbreeding coefficients=		=Estimation of individual inbreeding coefficients=
	Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output		Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

Albrecht: /* Site estimate of inbreeding coefficient (HWE test) */

2016-04-10T15:48:36Z

Site estimate of inbreeding coefficient (HWE test)

← Older revision		Revision as of 17:48, 10 April 2016
Line 3:		Line 3:
	;-HWE_pval_F		;-HWE_pval_F

	By choosing '''~~HWE_pval~~ 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hweF.gz''' file.		By choosing '''HWE_pval_F 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hweF.gz''' file.

	=Estimation of individual inbreeding coefficients=		=Estimation of individual inbreeding coefficients=
	Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output		Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

Albrecht: /* Site estimate of inbreeding coefficient (HWE test) */

2016-04-10T15:06:06Z

Site estimate of inbreeding coefficient (HWE test)

← Older revision		Revision as of 17:06, 10 April 2016
Line 1:		Line 1:
	=Site estimate of inbreeding coefficient (HWE test)=		=Site estimate of inbreeding coefficient (HWE test)=

	;-~~HWE_pval~~		;-HWE_pval_F

	~~By choosing '''HWE_pval 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hwe.gz''' file.~~


			By choosing '''HWE_pval 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hweF.gz''' file.

	=Estimation of individual inbreeding coefficients=		=Estimation of individual inbreeding coefficients=
	Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output		Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

Thorfinn: /* Estimation of individual inbreeding coefficients */

2014-02-28T11:52:18Z

Estimation of individual inbreeding coefficients

← Older revision		Revision as of 13:52, 28 February 2014
Line 8:		Line 8:

	=Estimation of individual inbreeding coefficients=		=Estimation of individual inbreeding coefficients=
	Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.		Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

	Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients.
	Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

Thorfinn at 11:51, 28 February 2014

2014-02-28T11:51:53Z

← Older revision		Revision as of 13:51, 28 February 2014
Line 1:		Line 1:
	~~ANGSD can~~ estimate ~~the 'F' on a single site basis.~~		=Site estimate of inbreeding coefficient (HWE test)=

	;-HWE_pval		;-HWE_pval
Line 5:		Line 5:
	By choosing '''HWE_pval 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hwe.gz''' file.		By choosing '''HWE_pval 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hwe.gz''' file.



			=Estimation of individual inbreeding coefficients=
	Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.		Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.

	Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients.		Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients.
	Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output		Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

Thorfinn at 11:50, 28 February 2014

2014-02-28T11:50:42Z

← Older revision		Revision as of 13:50, 28 February 2014
Line 9:		Line 9:
	Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients.		Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients.
	Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output		Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output


	~~;NB If in doubt if a specific analysis will work with inbreeding send an email.~~

Albrecht at 11:00, 7 February 2014

2014-02-07T11:00:02Z

← Older revision		Revision as of 13:00, 7 February 2014
Line 7:		Line 7:
	Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.		Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.

	Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating ~~per~~ individual inbreeding coefficients.		Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients.
	Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output		Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output


	;NB If in doubt if a specific analysis will work with inbreeding send an email.		;NB If in doubt if a specific analysis will work with inbreeding send an email.

Albrecht at 10:30, 7 February 2014

2014-02-07T10:30:12Z

← Older revision		Revision as of 12:30, 7 February 2014
Line 1:		Line 1:
	ANGSD can estimate the 'F' on a single site basis. ~~For method details see [[inbreed\|here]], this can be be used for an HWE test. This is done by using:~~		ANGSD can estimate the 'F' on a single site basis.

	;-HWE_pval		;-HWE_pval

Thorfinn at 14:28, 16 January 2014

2014-01-16T14:28:32Z

← Older revision		Revision as of 16:28, 16 January 2014
Line 12:		Line 12:

	;NB If in doubt if a specific analysis will work with inbreeding send an email.		;NB If in doubt if a specific analysis will work with inbreeding send an email.
	~~==HWE and Inbreeding estimates==~~

	~~And the most recent version of the stand alone program is here .~~

Thorfinn at 14:28, 16 January 2014

2014-01-16T14:28:10Z

← Older revision		Revision as of 16:28, 16 January 2014
Line 1:		Line 1:
	~~Filipe G~~. ~~Vieira has been extending the ANGSD feature set~~ by		ANGSD can estimate the 'F' on a single site basis. For method details see [[inbreed\|here]], this can be be used for an HWE test. This is done by using:
	~~# A method~~ for ~~estimating inbreeding (deviation from Hardy-Weinberg) based on output from ANGSD~~.
	# Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.		;-HWE_pval

			By choosing '''HWE_pval 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hwe.gz''' file.

			Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.

			Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating per individual inbreeding coefficients.
			Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output


	;NB If in doubt if a specific analysis will work with inbreeding send an email.		;NB If in doubt if a specific analysis will work with inbreeding send an email.
	==HWE and Inbreeding estimates==		==HWE and Inbreeding estimates==
	~~For method details see [[inbreed\|here]]~~
	And the most recent version of the stand alone program is here ~~https://github.com/fgvieira/ngsF~~.		And the most recent version of the stand alone program is here .