Minimac3 Info File - Revision history

Santy.8128: /* Dose2 */

2018-12-14T21:48:45Z

Dose2

← Older revision		Revision as of 17:48, 14 December 2018
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	Average [[ #LooDosage \| '''LooDosage''']] at haplotypes with alternate allele at this site. A value of 0.97 denotes that out of all the haplotypes with an alternate allele at this site, 97% of them would get imputed accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 1.0, more accurately has that site been imputed.		Average [[ #LooDosage \| '''LooDosage''']] at haplotypes with alternate allele at this site. A value of 0.97 denotes that out of all the haplotypes with an alternate allele at this site, 97% of them would get imputed accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 1.0, more accurately has that site been imputed.

	==='''~~Dose2~~'''===		==='''Dose1'''===

	One minus the average [[ #LooDosage \| '''LooDosage''']] at haplotypes with reference allele at this site. A value of 0.03 denotes that out of all the haplotypes with a reference allele at this site, 3% of them would get imputed in-accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 0.0, more accurately has that site been imputed.		One minus the average [[ #LooDosage \| '''LooDosage''']] at haplotypes with reference allele at this site. A value of 0.03 denotes that out of all the haplotypes with a reference allele at this site, 3% of them would get imputed in-accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 0.0, more accurately has that site been imputed.

Santy.8128: /* Dose1 */

2018-12-14T21:48:37Z

Dose1

← Older revision		Revision as of 17:48, 14 December 2018
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	While the '''LooRsq''' statistic completely ignores experimental genotypes, '''EmpR''' is calculated by calculating the correlation between the true genotyped values and the imputed dosages that were calculated by hiding all known genotyped for the given SNP (see [[ #LooDosage \| '''LooDosage''']]). A negative correlation between imputed and experimental genotypes can indicate allele flips. This statistic also can only be provided for genotyped sites. '''EmpRsq''' is the square of this correlation.		While the '''LooRsq''' statistic completely ignores experimental genotypes, '''EmpR''' is calculated by calculating the correlation between the true genotyped values and the imputed dosages that were calculated by hiding all known genotyped for the given SNP (see [[ #LooDosage \| '''LooDosage''']]). A negative correlation between imputed and experimental genotypes can indicate allele flips. This statistic also can only be provided for genotyped sites. '''EmpRsq''' is the square of this correlation.

	==='''~~Dose1~~'''===		==='''Dose0'''===

	Average [[ #LooDosage \| '''LooDosage''']] at haplotypes with alternate allele at this site. A value of 0.97 denotes that out of all the haplotypes with an alternate allele at this site, 97% of them would get imputed accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 1.0, more accurately has that site been imputed.		Average [[ #LooDosage \| '''LooDosage''']] at haplotypes with alternate allele at this site. A value of 0.97 denotes that out of all the haplotypes with an alternate allele at this site, 97% of them would get imputed accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 1.0, more accurately has that site been imputed.

Santy.8128: /* AvgCall */

2017-09-26T02:36:08Z

AvgCall

← Older revision		Revision as of 22:36, 25 September 2017
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	==='''AvgCall'''===		==='''AvgCall'''===

	This is the ~~allele frequency of alternate~~ (~~ALT~~) allele ~~from hard~~-~~call genotypes (see [[ #Hard Genotype\| '''Hard Genotype''']]) (allele with maximum posterior probability used instead~~ of ~~probability~~ of ~~alternate allele)~~		This is the average probability (certainty) of observing the most likely allele for each haplotype. While, the R-square is an measure of the confidence in the imputed dosages, the Average Call is a measure of confidence in the most-likely genotypes

	==='''Rsq'''===		==='''Rsq'''===

Santy.8128 at 00:47, 7 June 2016

2016-06-07T00:47:12Z

← Older revision		Revision as of 20:47, 6 June 2016
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	Minimac3 estimates imputed dosage at an haplotype level by finding the posterior probability of the alternate allele at that site. The genotype dosage is next evaluated as the sum of the haplotype dosages of each haplotype. For e.g. if the estimated posterior probability of the alternate allele is 0.98 and 0.96 in each haplotype, the genotype dosage is output as 0.98 + 0.97 = 1.95.		Minimac3 estimates imputed dosage at an haplotype level by finding the posterior probability of the alternate allele at that site. The genotype dosage is next evaluated as the sum of the haplotype dosages of each haplotype. For e.g. if the estimated posterior probability of the alternate allele is 0.98 and 0.96 in each haplotype, the genotype dosage is output as 0.98 + 0.97 = 1.95.


	= '''Hard Genotype''' =		= '''Hard Genotype''' =

	Minimac3 uses maximum likelihood estimator for hard-call genotypes. For each haplotype, the allele with the maximum posterior probability is assigned, and the final genotype call is obtained from the hard-call haplotypes. For e.g. if the estimated posterior probability of the alternate allele is 0.56 and 0.60 in each haplotype, then the alternate allele is assigned to each haplotype and the final hard-call genotype is output as 1\|1. Note that, the hard call genotype is NOT the MLE from the estimated genotype probabilities but instead from the estimated haplotype probabilities. For e.g. in this example, the posterior probability of the genotype 0\|1 is maximum and equal to 0.48, but the output hard genotype is not 0\|1 but 1\|1, because at the haplotype level, each haplotype had more than 50% probability of alternate allele. As it is obvious, such cases will only arise when the sites are not imputed well.		Minimac3 uses maximum likelihood estimator for hard-call genotypes. For each haplotype, the allele with the maximum posterior probability is assigned, and the final genotype call is obtained from the hard-call haplotypes. For e.g. if the estimated posterior probability of the alternate allele is 0.56 and 0.60 in each haplotype, then the alternate allele is assigned to each haplotype and the final hard-call genotype is output as 1\|1. Note that, the hard call genotype is NOT the MLE from the estimated genotype probabilities but instead from the estimated haplotype probabilities. For e.g. in this example, the posterior probability of the genotype 0\|1 is maximum and equal to 0.48, but the output hard genotype is not 0\|1 but 1\|1, because at the haplotype level, each haplotype had more than 50% probability of alternate allele. As it is obvious, such cases will only arise when the sites are not imputed well.


	= '''LooDosage''' =		= '''LooDosage''' =


	Minimac3 uses an ad-hoc method to estimate imputation accuracy at sites that were genotyped in the study sample. For each such genotyped site, Minimac3 hides all known genotypes for that site and calculates an imputed dosage (in addition to the usual alternate allele dosage calculated assuming the genotypes are known at the site). This special imputed value is called Leave-One-Out dosage ('''LooDosage''') and is only available for genotyped sites. '''LooDosage''' is used to calculate Empirical-Rsquare ('''EmpR''', '''EmpRsq''') by directly calculating the Pearson correlation coefficient between '''LooDosage'''and known genotypes. It is also used to estimate the '''LooRsq'''.		Minimac3 uses an ad-hoc method to estimate imputation accuracy at sites that were genotyped in the study sample. For each such genotyped site, Minimac3 hides all known genotypes for that site and calculates an imputed dosage (in addition to the usual alternate allele dosage calculated assuming the genotypes are known at the site). This special imputed value is called Leave-One-Out dosage ('''LooDosage''') and is only available for genotyped sites. '''LooDosage''' is used to calculate Empirical-Rsquare ('''EmpR''', '''EmpRsq''') by directly calculating the Pearson correlation coefficient between '''LooDosage'''and known genotypes. It is also used to estimate the '''LooRsq'''.

Santy.8128: /* Info File Descriptors */

2016-06-07T00:46:45Z

Info File Descriptors

← Older revision		Revision as of 20:46, 6 June 2016
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	==='''ALT_Frq'''===		==='''ALT_Frq'''===

	This is the allele frequency of alternate (ALT) allele in the imputed dosage data (see [[ #Dosage\| '''Dosage''']])).		This is the allele frequency of alternate (ALT) allele in the imputed dosage data (see [[ #Dosage\| '''Dosage''']]).

	==='''MAF'''===		==='''MAF'''===
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	==='''AvgCall'''===		==='''AvgCall'''===

	This is the allele frequency of alternate (ALT) allele from hard-call genotypes (see [[ #Hard Genotype\| '''Hard Genotype''']])) (allele with maximum posterior probability used instead of probability of alternate allele)		This is the allele frequency of alternate (ALT) allele from hard-call genotypes (see [[ #Hard Genotype\| '''Hard Genotype''']]) (allele with maximum posterior probability used instead of probability of alternate allele)

	==='''Rsq'''===		==='''Rsq'''===

Santy.8128: /* REF(0), ALT(1) */

2016-06-07T00:46:32Z

REF(0), ALT(1)

← Older revision		Revision as of 20:46, 6 June 2016
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	==='''REF(0)''', '''ALT(1)'''===		==='''REF(0)''', '''ALT(1)'''===

	These are the reference and alternate alleles for the variant as imported from the reference panel file (either VCF or M3VCF). The dosage value (see [[ #Dosage\| '''Dosage''']])) in the <code>.dose</code> file is the alternate allele dosage and NOT major allele dosage as in earlier versions of '''minimac'''. Specifcally, the dosage denotes the probability <code>P(REF,ALT) + 2*P(ALT,ALT)</code>.		These are the reference and alternate alleles for the variant as imported from the reference panel file (either VCF or M3VCF). The dosage value (see [[ #Dosage\| '''Dosage''']]) in the <code>.dose</code> file is the alternate allele dosage and NOT major allele dosage as in earlier versions of '''minimac'''. Specifcally, the dosage denotes the probability <code>P(REF,ALT) + 2*P(ALT,ALT)</code>.

	==='''ALT_Frq'''===		==='''ALT_Frq'''===

Santy.8128: /* Rsq */

2016-06-07T00:46:24Z

Rsq

← Older revision		Revision as of 20:46, 6 June 2016
Line 35:		Line 35:
	This is the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically <math>2p</math> where <math>p</math> is the frequency of the allele being imputed.		This is the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically <math>2p</math> where <math>p</math> is the frequency of the allele being imputed.

	Currently, Minimac3 uses the following definition (where <math>\hat{p}</math> is the alternate allele frequency and <math>D_i</math> is the imputed alternate allele probability at the <math>i^{th}</math> haplotype (see [[ #Dosage\| '''Dosage''']])) and <math>n</math> is the number of GWAS samples) :		Currently, Minimac3 uses the following definition (where <math>\hat{p}</math> is the alternate allele frequency and <math>D_i</math> is the imputed alternate allele probability at the <math>i^{th}</math> haplotype (see [[ #Dosage\| '''Dosage''']]) and <math>n</math> is the number of GWAS samples) :

	:<math>\hat{r}^2 = {{ {{1}\over{2n}} \times \sum_{i=1}^{2n} {(D_i - \hat{p})^2} }\over{\hat{p}(1-\hat{p})}}</math>		:<math>\hat{r}^2 = {{ {{1}\over{2n}} \times \sum_{i=1}^{2n} {(D_i - \hat{p})^2} }\over{\hat{p}(1-\hat{p})}}</math>

Santy.8128: /* Info File Descriptors */

2016-06-07T00:46:13Z

Info File Descriptors

← Older revision		Revision as of 20:46, 6 June 2016
Line 17:		Line 17:
	==='''REF(0)''', '''ALT(1)'''===		==='''REF(0)''', '''ALT(1)'''===

	These are the reference and alternate alleles for the variant as imported from the reference panel file (either VCF or M3VCF). The dosage value in the <code>.dose</code> file is the alternate allele dosage and NOT major allele dosage as in earlier versions of '''minimac'''. Specifcally, the dosage denotes the probability <code>P(REF,ALT) + 2*P(ALT,ALT)</code>.		These are the reference and alternate alleles for the variant as imported from the reference panel file (either VCF or M3VCF). The dosage value (see [[ #Dosage\| '''Dosage''']])) in the <code>.dose</code> file is the alternate allele dosage and NOT major allele dosage as in earlier versions of '''minimac'''. Specifcally, the dosage denotes the probability <code>P(REF,ALT) + 2*P(ALT,ALT)</code>.

	==='''ALT_Frq'''===		==='''ALT_Frq'''===

	This is the allele frequency of alternate (ALT) allele in the imputed dosage data.		This is the allele frequency of alternate (ALT) allele in the imputed dosage data (see [[ #Dosage\| '''Dosage''']])).

	==='''MAF'''===		==='''MAF'''===
Line 29:		Line 29:
	==='''AvgCall'''===		==='''AvgCall'''===

	This is the allele frequency of alternate (ALT) allele ~~in the assuming~~ hard-call genotypes (allele with maximum posterior probability used instead of probability of alternate allele)		This is the allele frequency of alternate (ALT) allele from hard-call genotypes (see [[ #Hard Genotype\| '''Hard Genotype''']])) (allele with maximum posterior probability used instead of probability of alternate allele)

	==='''Rsq'''===		==='''Rsq'''===
Line 35:		Line 35:
	This is the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically <math>2p</math> where <math>p</math> is the frequency of the allele being imputed.		This is the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically <math>2p</math> where <math>p</math> is the frequency of the allele being imputed.

	Currently, Minimac3 uses the following definition (where <math>\hat{p}</math> is the alternate allele frequency and <math>D_i</math> is the imputed alternate allele probability at the <math>i^{th}</math> haplotype and <math>n</math> is the number of GWAS samples) :		Currently, Minimac3 uses the following definition (where <math>\hat{p}</math> is the alternate allele frequency and <math>D_i</math> is the imputed alternate allele probability at the <math>i^{th}</math> haplotype (see [[ #Dosage\| '''Dosage''']])) and <math>n</math> is the number of GWAS samples) :

	:<math>\hat{r}^2 = {{ {{1}\over{2n}} \times \sum_{i=1}^{2n} {(D_i - \hat{p})^2} }\over{\hat{p}(1-\hat{p})}}</math>		:<math>\hat{r}^2 = {{ {{1}\over{2n}} \times \sum_{i=1}^{2n} {(D_i - \hat{p})^2} }\over{\hat{p}(1-\hat{p})}}</math>

Santy.8128: /* LooDosage */

2016-06-07T00:43:11Z

LooDosage

← Older revision		Revision as of 20:43, 6 June 2016
Line 58:		Line 58:

	One minus the average [[ #LooDosage \| '''LooDosage''']] at haplotypes with reference allele at this site. A value of 0.03 denotes that out of all the haplotypes with a reference allele at this site, 3% of them would get imputed in-accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 0.0, more accurately has that site been imputed.		One minus the average [[ #LooDosage \| '''LooDosage''']] at haplotypes with reference allele at this site. A value of 0.03 denotes that out of all the haplotypes with a reference allele at this site, 3% of them would get imputed in-accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 0.0, more accurately has that site been imputed.

			= '''Dosage''' =

			Minimac3 estimates imputed dosage at an haplotype level by finding the posterior probability of the alternate allele at that site. The genotype dosage is next evaluated as the sum of the haplotype dosages of each haplotype. For e.g. if the estimated posterior probability of the alternate allele is 0.98 and 0.96 in each haplotype, the genotype dosage is output as 0.98 + 0.97 = 1.95.


			= '''Hard Genotype''' =

			Minimac3 uses maximum likelihood estimator for hard-call genotypes. For each haplotype, the allele with the maximum posterior probability is assigned, and the final genotype call is obtained from the hard-call haplotypes. For e.g. if the estimated posterior probability of the alternate allele is 0.56 and 0.60 in each haplotype, then the alternate allele is assigned to each haplotype and the final hard-call genotype is output as 1\|1. Note that, the hard call genotype is NOT the MLE from the estimated genotype probabilities but instead from the estimated haplotype probabilities. For e.g. in this example, the posterior probability of the genotype 0\|1 is maximum and equal to 0.48, but the output hard genotype is not 0\|1 but 1\|1, because at the haplotype level, each haplotype had more than 50% probability of alternate allele. As it is obvious, such cases will only arise when the sites are not imputed well.


	= '''LooDosage''' =		= '''LooDosage''' =

Santy.8128: /* AvgCall */

2016-06-07T00:33:51Z

AvgCall

← Older revision		Revision as of 20:33, 6 June 2016
Line 29:		Line 29:
	==='''AvgCall'''===		==='''AvgCall'''===

	-		This is the allele frequency of alternate (ALT) allele in the assuming hard-call genotypes (allele with maximum posterior probability used instead of probability of alternate allele)

	==='''Rsq'''===		==='''Rsq'''===