Allele Frequencies - Revision history

Isin: /* Output data */

2023-06-08T10:16:21Z

Output data

← Older revision		Revision as of 12:16, 8 June 2023
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	is the number of individuals with data		is the number of individuals with data
	;pK-EM		;pK-EM
	~~probability~~ of ~~a site being SNP with~~ known minor ~~alleles~~ (-doSNPStat 1 -doMaf 1)		p-value for the frequency of (known) minor allele (-doSNPStat 1 -doMaf 1)
	;pu-EM		;pu-EM
	p-value for ~~a site being SNP with~~ unknown minor ~~alleles~~ (-doSNPStat 1 -doMaf 2)		p-value for the frequency of (unknown) minor allele (-doSNPStat 1 -doMaf 2)

Isin: /* .mafs.gz */

2023-06-08T07:55:20Z

.mafs.gz

← Older revision		Revision as of 09:55, 8 June 2023
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	is the number of individuals with data		is the number of individuals with data
	;pK-EM		;pK-EM
	probability of a site being SNP (~~using~~ -doSNPStat 1 ~~and~~ -doMaf 1)		probability of a site being SNP with known minor alleles (-doSNPStat 1 -doMaf 1)
	;pu-EM		;pu-EM
	~~probability of~~ a site being SNP (~~using~~ -doSNPStat 1 ~~and~~ -doMaf 2)		p-value for a site being SNP with unknown minor alleles (-doSNPStat 1 -doMaf 2)

Isin: /* .mafs.gz */

2023-06-07T14:03:33Z

.mafs.gz

← Older revision		Revision as of 16:03, 7 June 2023
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	;nInd		;nInd
	is the number of individuals with data		is the number of individuals with data
			;pK-EM
			probability of a site being SNP (using -doSNPStat 1 and -doMaf 1)
			;pu-EM
			probability of a site being SNP (using -doSNPStat 1 and -doMaf 2)

Albrecht: /* Brief Overview */

2023-02-06T16:22:40Z

Brief Overview

← Older revision		Revision as of 18:22, 6 February 2023
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	<pre>		<pre>
	./angsd -doMaf		./angsd -doMaf
	~~-> angsd version: 0.910-76-gad32889 (htslib: 1.3-32-gecdc348) build(Mar 2 2016 12:38:33)~~
	~~-> Analysis helpbox/synopsis information:~~
	~~-> Command:~~
	~~./angsd -doMaf -> Wed Mar 2 12:45:40 2016~~
	~~------------------------~~
	abcFreq.cpp:		abcFreq.cpp:
	-doMaf 0 (Calculate persite frequencies '.mafs.gz')		-doMaf 0 (Calculate persite frequencies '.mafs.gz')
	1: Frequency (fixed major and minor)		1: Frequency (fixed major and minor)
	2: Frequency (fixed major unknown minor)		2: Frequency (fixed major unknown minor)
	4: Frequency from genotype probabilities		4: Frequency from genotype probabilities
	8: AlleleCounts based method (known major minor)		8: AlleleCounts based method (known major minor)
	NB. Filedumping is supressed if value is negative		NB. Filedumping is supressed if value is negative
	-doPost 0 (Calculate posterior prob 3xgprob)		-doPost 0 (Calculate posterior prob 3xgprob)
	1: Using frequency as prior		1: Using frequency as prior
	2: Using uniform prior		2: Using uniform prior
	3: Using SFS as prior (still in development)		3: Using SFS as prior (still in development)
			4: Using reference panel as prior (still in development), requires a site file with chr pos major minor af ac an
	Filters:		Filters:
	-minMaf -1.000000 (Remove sites with MAF below)		-minMaf -1.000000 (Remove sites with MAF below)
	-SNP_pval 1.~~000000~~ (Remove sites with a pvalue larger)		-SNP_pval 0.317311 (Remove sites with a pvalue larger)
	-rmTriallelic 0.000000 (Remove sites with a pvalue lower)		-rmSNPs 0 (Remove infered SNPs instead of keeping them (pval > SNP_pval)
			-rmTriallelic 0.000000 (Remove sites with a pvalue lower)
			-forceMaf 0 (Write .mafs file when running -doAsso (by default does not output .mafs file with -doAsso))
			-skipMissing 1 (Set post to 0.33 if missing (do not use freq as prior))
	Extras:		Extras:
	-ref (null) (Filename for fasta reference)		-ref (null) (Filename for fasta reference)
	-anc (null) (Filename for fasta ancestral)		-anc (null) (Filename for fasta ancestral)
	-eps 0.001000 [Only used for -doMaf &8]		-eps 0.001000 [Only used for -doMaf &8]
	-beagleProb 0 (Dump beagle style postprobs)		-beagleProb 0 (Dump beagle style postprobs)
	-indFname (null) (file containing individual inbreedcoeficients)		-indFname (null) (file containing individual inbreedcoeficients)
			-underFlowProtect 0 (file containing individual inbreedcoeficients)
	NB These frequency estimators requires major/minor -doMajorMinor		NB These frequency estimators requires major/minor -doMajorMinor

	</pre>		</pre>

Albrecht at 09:00, 28 September 2021

2021-09-28T09:00:16Z

← Older revision		Revision as of 11:00, 28 September 2021
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	<pre>		<pre>
	./angsd -out out -doMajorMinor 1 -doMaf 3 -bam bam.filelist -GL 1		./angsd -out out -doMajorMinor 1 -doMaf 3 -bam bam.filelist -GL 2
	</pre>		</pre>

Albrecht at 09:53, 2 April 2018

2018-04-02T09:53:41Z

← Older revision		Revision as of 11:53, 2 April 2018
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	<div class="keywords"> domaf, dopost, SNP_pval </div>		<div class="keywords"> -domaf,-domaf,-domaf,-domaf,-domaf, domaf, domaf, domaf, domaf, domaf, domaf, dopost, SNP_pval </div>

	The allele frequency is the relative frequency of an allele for a site. This can be polarized according to the major/minor, reference/non-refernce or ancestral/derived. .Therefore the choice of allele frequency estimator is closely related to choosing which alleles are segregating (see [[Inferring_Major_and_Minor_alleles]]).		The allele frequency is the relative frequency of an allele for a site. This can be polarized according to the major/minor, reference/non-refernce or ancestral/derived. .Therefore the choice of allele frequency estimator is closely related to choosing which alleles are segregating (see [[Inferring_Major_and_Minor_alleles]]).

Albrecht at 09:49, 2 April 2018

2018-04-02T09:49:05Z

← Older revision		Revision as of 11:49, 2 April 2018
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			<div class="keywords"> domaf, dopost, SNP_pval </div>

	The allele frequency is the relative frequency of an allele for a site. This can be polarized according to the major/minor, reference/non-refernce or ancestral/derived. .Therefore the choice of allele frequency estimator is closely related to choosing which alleles are segregating (see [[Inferring_Major_and_Minor_alleles]]).		The allele frequency is the relative frequency of an allele for a site. This can be polarized according to the major/minor, reference/non-refernce or ancestral/derived. .Therefore the choice of allele frequency estimator is closely related to choosing which alleles are segregating (see [[Inferring_Major_and_Minor_alleles]]).

Thorfinn: /* Brief Overview */

2016-03-02T11:46:00Z

Brief Overview

← Older revision		Revision as of 13:46, 2 March 2016
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	<pre>		<pre>
	~~Command:~~		./angsd -doMaf
	./angsd -doMaf		-> angsd version: 0.910-76-gad32889 (htslib: 1.3-32-gecdc348) build(Mar 2 2016 12:38:33)
	-> angsd version: 0.~~576~~ build(~~Jan 16 2014 01~~:49:06)		-> Analysis helpbox/synopsis information:
	-> Analysis helpbox/synopsis information:		-> Command:
			./angsd -doMaf -> Wed Mar 2 12:45:40 2016
	------------------------		------------------------
	~~analysisMaf~~.cpp:		abcFreq.cpp:
	-doMaf 0 (Calculate persite frequencies '.mafs.gz')		-doMaf 0 (Calculate persite frequencies '.mafs.gz')
	1: Frequency (fixed major and minor)		1: Frequency (fixed major and minor)
	2: Frequency (fixed major unknown minor)		2: Frequency (fixed major unknown minor)
	4: Frequency from genotype probabilities		4: Frequency from genotype probabilities
	8: AlleleCounts based method (known major minor)		8: AlleleCounts based method (known major minor)
	NB. Filedumping is supressed if value is negative		NB. Filedumping is supressed if value is negative
	-doPost 0 (Calculate posterior prob 3xgprob)		-doPost 0 (Calculate posterior prob 3xgprob)
	1: Using frequency as prior		1: Using frequency as prior
	2: Using uniform prior		2: Using uniform prior
			3: Using SFS as prior (still in development)
	Filters:		Filters:
	-minMaf 0.000000 (Remove sites with MAF below)		-minMaf -1.000000 (Remove sites with MAF below)
	-SNP_pval 1.000000 (Remove sites with a pvalue larger)		-SNP_pval 1.000000 (Remove sites with a pvalue larger)
			-rmTriallelic 0.000000 (Remove sites with a pvalue lower)
	Extras:		Extras:
	-ref (null) (Filename for fasta reference)		-ref (null) (Filename for fasta reference)
	-anc (null) (Filename for fasta ancestral)		-anc (null) (Filename for fasta ancestral)
	-eps 0.001000 [Only used for -doMaf &8]		-eps 0.001000 [Only used for -doMaf &8]
	-beagleProb 0 (Dump beagle style postprobs)		-beagleProb 0 (Dump beagle style postprobs)
	-indFname (null) (file containing individual inbreedcoeficients)		-indFname (null) (file containing individual inbreedcoeficients)
	NB These frequency estimators requires major/minor -doMajorMinor		NB These frequency estimators requires major/minor -doMajorMinor
	</pre>		</pre>

Thorfinn: /* Allele Frequency estimation */

2014-03-05T15:25:11Z

Allele Frequency estimation

← Older revision		Revision as of 17:25, 5 March 2014
Line 57:		Line 57:

	Multiple estimators can be used simultaniusly be summing up the above numbers. Thus -doMaf 7 (1+2+4) will use the first three estimators. If the allele frequencies are estimated from the genotype likelihoods then you need to infer the major and minor allele (-doMajorMinor)		Multiple estimators can be used simultaniusly be summing up the above numbers. Thus -doMaf 7 (1+2+4) will use the first three estimators. If the allele frequencies are estimated from the genotype likelihoods then you need to infer the major and minor allele (-doMajorMinor)

			;NB using -doMaf 4 is only supported if the posteriors are supplied as external files. Since the estimation of genotype posteriors in itself requires a maf estimator.

	=Example=		=Example=

Albrecht: /* .mafs */

2014-02-26T16:43:47Z

.mafs

← Older revision		Revision as of 18:43, 26 February 2014
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	=Output data=		=Output data=
	==.mafs==		==.mafs.gz==
	<pre>		<pre>
	chromo position major minor ref knownEM unknownEM nInd		chromo position major minor ref knownEM unknownEM nInd
Line 100:		Line 100:

	</pre>		</pre>
	~~The first 4 columns are always defined to be:~~

	;chromo		;chromo