Question: Inferring pedigree from SNP genotyping data
gravatar for Selenocysteine
5.8 years ago by
Dublin, Ireland
Selenocysteine600 wrote:

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 • 2.5k views
ADD COMMENTlink modified 5.8 years ago by alesssia570 • written 5.8 years ago by Selenocysteine600
gravatar for alesssia
5.8 years ago by
London, UK
alesssia570 wrote:

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.

ADD COMMENTlink written 5.8 years ago by alesssia570

Thank you :)

ADD REPLYlink written 5.8 years ago by Selenocysteine600
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