ANGSD: Analysis of next generation Sequencing Data
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== NGSrelate - estimation of | == NGSrelate - estimation of IBD probabilities == | ||
In order to estimate kinship coefficient then population allele frequencies are needed. These can be estimated from data if you can multiple individuals. For some individuals, for example most human populations, there are publicly available data. | In order to estimate kinship coefficient then population allele frequencies are needed. These can be estimated from data if you can multiple individuals. For some individuals, for example most human populations, there are publicly available data. | ||
If you can obtain population allele frequencies then we recommend that you use NGSrelate. | If you can obtain population allele frequencies or have a many samples from your population then we recommend that you use NGSrelate has works with ANGSD output. From the estimated IBD probabilities you can then infer the relationship. Below is a table of the expected IBD sharing probabilities assuming no inbreeding | ||
{| class="wikitable" style="text-align: center | |||
!| Relationship || <math>K_0</math>|| <math>K_1</math> || <math>K_2</math> | |||
|- | |||
| Parent-Offspring || <math>0 </math> || <math>1</math> || <math>0 </math> | |||
|- | |||
| Full siblings || <math>0.25 </math> || <math> 0.5 </math> || <math> 0.25 </math> | |||
|- | |||
| Half siblings || <math> 0.5 </math> || <math>0.5 </math> || <math> 0 </math> | |||
|- | |||
| First cousins || <math>0.75 </math> || <math>0.25 </math> || <math> 0 </math> | |||
|} | |||
NGSrelate has its very own website http://www.popgen.dk/software/index.php/NgsRelate | NGSrelate has its very own website http://www.popgen.dk/software/index.php/NgsRelate | ||
Revision as of 13:53, 12 July 2016
NGSrelate - estimation of IBD probabilities
In order to estimate kinship coefficient then population allele frequencies are needed. These can be estimated from data if you can multiple individuals. For some individuals, for example most human populations, there are publicly available data. If you can obtain population allele frequencies or have a many samples from your population then we recommend that you use NGSrelate has works with ANGSD output. From the estimated IBD probabilities you can then infer the relationship. Below is a table of the expected IBD sharing probabilities assuming no inbreeding
| Relationship | |||
|---|---|---|---|
| Parent-Offspring | |||
| Full siblings | |||
| Half siblings | |||
| First cousins |
NGSrelate has its very own website http://www.popgen.dk/software/index.php/NgsRelate
IBS/genotype distribution
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.