Relatedness - Revision history

Albrecht at 07:21, 29 August 2019

2019-08-29T07:21:44Z

← Older revision		Revision as of 09:21, 29 August 2019
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	If you do not have population allele frequencies the you cannot estimate kinship coefficients. However, you can still make some claims about the relationship of your samples based on IBS patterns. Below is an example of IBS patterns between two individuals where we ignore the allele types. G is the genotype that counts for example the number of derived or non-reference alleles. Basically it is the 2D SFS where the is just 1 individual in each of the two populations		If you do not have population allele frequencies the you cannot estimate kinship coefficients. However, you can still make some claims about the relationship of your samples based on IBS patterns. Below is an example of IBS patterns between two individuals where we ignore the allele types. G is the genotype that counts for example the number of derived or non-reference alleles. Basically it is the 2D SFS where the is just 1 individual in each of the two populations
			The full decription of the method can be seen here: [http://www.popgen.dk/software/index.php/IBSrelate IBSrelate]

	{\| class="wikitable" style="text-align: center		{\| class="wikitable" style="text-align: center

Albrecht: /* IBS/genotype distribution */

2016-07-14T14:46:31Z

IBS/genotype distribution

← Older revision		Revision as of 16:46, 14 July 2016
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	\| Parent-Offspring \|\| <math>C,G=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}=0.5 </math> \|\| -		\| Parent-Offspring \|\| <math>C,G=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}=0.5 </math> \|\| -
	\|-		\|-
	\| Full siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}>0.5 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<10/13 </math>		\| Full siblings \|\| <math> \frac{E}{C+G}>10 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}>0.5 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<10/13 </math>
	\|-		\|-
	\| Half siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/9</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/6</math>		\| Half siblings \|\| <math> \frac{E}{C+G}>4 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/9</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/6</math>
	\|-		\|-
	\| First cousins \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<8/19</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/14 </math>		\| First cousins \|\| <math> \frac{E}{C+G}>8/3 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<8/19</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/14 </math>
	\|-		\|-
	\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0 </math>		\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0 </math>

Albrecht: /* IBS/genotype distribution */

2016-07-12T14:28:02Z

IBS/genotype distribution

← Older revision		Revision as of 16:28, 12 July 2016
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	{\| class="wikitable" style="text-align: center		{\| class="wikitable" style="text-align: center
	!\| Relationship \|\| Expected ratio \|\| Expected ratio \|\| Expected ratio		!\| Relationship \|\| Expected ratio \|\| Expected ratio (R1) \|\| Expected ratio (R1)
	\|-		\|-
	\| mono-zygotic twin \|\| <math>B,C,D,F,G,H=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}= \infty </math> \|\| -		\| mono-zygotic twin \|\| <math>B,C,D,F,G,H=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}= \infty </math> \|\| -
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	\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0 </math>		\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0 </math>
	\|}		\|}


			[[File:ratioRel.png\|800px]]

	=== How to get the IBS pattern ===		=== How to get the IBS pattern ===

Albrecht: /* IBS/genotype distribution */

2016-07-12T14:02:08Z

IBS/genotype distribution

← Older revision		Revision as of 16:02, 12 July 2016
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			Here are some usefull ratio of IBS that can be used to say something about relatedness. Here we assume no inbreeding.

	{\| class="wikitable" style="text-align: center		{\| class="wikitable" style="text-align: center
	!\| Relationship \|\| Expected ratio \|\| ~~other~~ \|\|		!\| Relationship \|\| Expected ratio \|\| Expected ratio \|\| Expected ratio
	\|-		\|-
	\| mono-zygotic twin \|\| <math>B,C,D,F,G,H=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}= \infty </math> \|\| -		\| mono-zygotic twin \|\| <math>B,C,D,F,G,H=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}= \infty </math> \|\| -

Albrecht: /* How to get the IBS pattern */

2016-07-12T13:58:54Z

How to get the IBS pattern

← Older revision		Revision as of 15:58, 12 July 2016
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	=== How to get the IBS pattern ===		=== How to get the IBS pattern ===

	You can get the estimate by using the [[2d_SFS_Estimation\| 2D SFS method]] or you can use the [[Genotype_Distribution\| genotype distribution method]] both in ANGSD		You can get the estimate by using the [[2d_SFS_Estimation\| 2D SFS method]] or you can use the [[Genotype_Distribution\| genotype distribution method]] both in ANGSD.

			The two methods are very similar but with a very small difference. The SFS method uses ancestral information or a reference in order to infer the 2 alleles for each position. The genotype distribution does not infer either the major or the minor allele but uses all 10 possible genotype likelihoods.

	=== Rcode to get expectations===		=== Rcode to get expectations===

Albrecht at 13:55, 12 July 2016

2016-07-12T13:55:44Z

← Older revision		Revision as of 15:55, 12 July 2016
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	=== How to get the IBS pattern ===		=== How to get the IBS pattern ===

	You can get the estimate by using the [[2d_SFS_Estimation 2D\|SFS method]] or you can use the [[~~genotype_distribution~~\|genotype distribution method]] both in ANGSD		You can get the estimate by using the [[2d_SFS_Estimation\| 2D SFS method]] or you can use the [[Genotype_Distribution\| genotype distribution method]] both in ANGSD

Albrecht: /* IBS/genotype distribution */

2016-07-12T13:53:00Z

IBS/genotype distribution

← Older revision		Revision as of 15:53, 12 July 2016
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	\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0 </math>		\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0 </math>
	\|}		\|}
			=== How to get the IBS pattern ===

			You can get the estimate by using the [[2d_SFS_Estimation 2D\|SFS method]] or you can use the [[genotype_distribution\|genotype distribution method]] both in ANGSD


			=== Rcode to get expectations===
	<pre>		<pre>
	#R code go get expected IBS pattern		# R code go get expected IBS pattern
			## k is the 3 IBD sharing probabities
			## f is the allele frequency
	getEst<-function(k=c(1,0,0),f=0.5){		getEst<-function(k=c(1,0,0),f=0.5){
	p<-f		p<-f

Albrecht at 13:47, 12 July 2016

2016-07-12T13:47:09Z

← Older revision		Revision as of 15:47, 12 July 2016
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	\| Half siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/9</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/6</math>		\| Half siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/9</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/6</math>
	\|-		\|-
	\| First cousins \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<8/19</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/14		\| First cousins \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<8/19</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/14 </math>
	\|-		\|-
	\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0		\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0 </math>
	\|}		\|}

Albrecht: /* IBS/genotype distribution */

2016-07-12T13:46:45Z

IBS/genotype distribution

← Older revision		Revision as of 15:46, 12 July 2016
Line 57:		Line 57:
	\| Half siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/9</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/6</math>		\| Half siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/9</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/6</math>
	\|-		\|-
	\| First cousins \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> <~~math>0.25~~ </math> \|\| <math> ~~0 <~~/~~math>~~		\| First cousins \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<8/19</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/14
	\|-		\|-
	\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> <~~math>0~~ </math> \|\| <math> 0 ~~</math>~~		\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/10</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 0
	\|}		\|}

Albrecht: /* IBS/genotype distribution */

2016-07-12T13:43:46Z

IBS/genotype distribution

← Older revision		Revision as of 15:43, 12 July 2016
Line 47:		Line 47:

	{\| class="wikitable" style="text-align: center		{\| class="wikitable" style="text-align: center
	!\| Relationship \|\| Expected ratio \|\| \|\|		!\| Relationship \|\| Expected ratio \|\| other \|\|
	\|-		\|-
	\| mono-zygotic twin \|\| <math>B,C,D,F,G,H=0 </math> \|\| <math>0</math> \|\| ~~<math>1 </math>~~		\| mono-zygotic twin \|\| <math>B,C,D,F,G,H=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}= \infty </math> \|\| -
	\|-		\|-
	\| Parent-Offspring \|\| <math>C,G=0 </math> \|\| <math>1</math> \|\| ~~<math>0 </math>~~		\| Parent-Offspring \|\| <math>C,G=0 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}=0.5 </math> \|\| -
	\|-		\|-
	\| Full siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> 0.5 </math> \|\| <math> ~~0.25~~ </math>		\| Full siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}>0.5 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<10/13 </math>
	\|-		\|-
	\| Half siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math>~~0.5~~ </math> \|\| <math> 0 </math>		\| Half siblings \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> \frac{E}{B+C+D+F+G+H}<4/9</math> \|\| <math> \frac{E}{B+C+D+F+G+H}> 1/6</math>
	\|-		\|-
	\| First cousins \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math>0.25 </math> \|\| <math> 0 </math>		\| First cousins \|\| <math> \frac{E}{C+G}>2 </math> \|\| <math> <math>0.25 </math> \|\| <math> 0 </math>
	\|-		\|-
	\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math>0 </math> \|\| <math> 0 </math>		\| Unrelated \|\| <math> \frac{E}{C+G}=2 </math> \|\| <math> <math>0 </math> \|\| <math> 0 </math>
	\|}		\|}