This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Inferring pedigree from SNP genotyping data

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

snp pedigree
• 3,778 views • link
updated by Ram Ram • written by Selenocysteine Selenocysteine

1 answer

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.

• 0 views • link
updated by Ram Ram • written by alesssia alesssia

Log in to answer this question.

More posts like this