Inferring pedigree from SNP genotyping data

Question

[Selenocysteine]

Hello everyone,

I have a set of F2 mice families, which were genotyped with a genome-wide coverage with an Illumina Golden Gate Genotyping Assay. However, due to the problems during the breeding of mice, I miss data about which mice are the parents of some of the F1 individuals. Is there any software which can help me build their pedigree, based on SNP genotyping data?

Thank you

Answer 1

[alesssia]

You could check the relatedness (kinship) coefficients among your mice. You can evaluate the IBS with PLINK or with EMMAx (EMMAx also evaluates the BM matrix). Otherwise you can evaluate the genetic relationship matrix (GRM) with GCTA.

[Selenocysteine]

Thank you :)