Identify putative parent offspring within a population
This script examines the frequency of pedigree inconsistent loci, that is, those loci that are homozygotes in the parent for the reference allele, and homozygous in the offspring for the alternate allele. This condition is not consistent with any pedigree, regardless of the (unkonwn) genotype of the other parent. The pedigree inconsistent loci are counted as an indication of whether or not it is reasonable to propose the two individuals are in a parent-offspring relationship.
gl.report.parent.offspring( x, min.rdepth = 12, min.reproducibility = 1, range = 1.5, verbose = NULL )
x |
Name of the genlight object containing the SNP genotypes [required] |
min.rdepth |
Minimum read depth to include in analysis [default = 12] |
min.reproducibility |
Minimum reproducibility to include in analysis [default = 1] |
range |
– specifies the range to extend beyond the interquartile range for delimiting outliers [default = 1.5 interquartile ranges] |
verbose |
– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity] |
Obviously, if the two individuals are in a parent offspring relationship, the true number of pedigree inconsistent loci should be zero, but SNP calling is not infallible. Some loci will be mis-called. The problem thus becomes one of determining if the two focal individuals have a count of pedigree inconsistent loci less than would be expected of typical unrelated individuals. There are some quite sophisticated software packages available to formally apply likelihoods to the decision, but we use a simple outlier comparison.
To reduce the frequency of mis-calls, and so emphasise the difference between true parent-offspring pairs and unrelated pairs, the data can be filtered on read depth. Typically minimum read depth is set to 5x, but you can examine the distribution of read depths with gl.report.rdepth() and push this up with an acceptable loss of loci. 12x might be a good minimum for this particular analysis. It is sensible also to push the minimum reproducibility up to 1, if that does not result in an unacceptable loss of loci.
Note that the null expectation is not well defined, and the power reduced, if the population from which the putative parent-offspring pairs are drawn contains many sibs. Note also that if an individual has been genotyped twice in the dataset, the replicate pair will be assessed by this script as being in a parent-offspring relationship.
A set of individuals in parent-offspring relationship
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