I do have an offspring of plants. In theory it should be biparental. The plant is a strict outcrossing plant. However, I fear that about 30% are offspring from the selfed mothers plant. (Own quick and dirty analysis using the GBS data of available high quality markers (n ~ 1000))
Is there an already published tool for checking this?
I have the genotypic data for the parents and all offspring plants (GBS data, vcf file).
At he end this might be interesting for quality issues of the input data for a QTL study and eventually for the exclusion of individuals.
See attached: one SNP marker of this offspring with the relative frequency of callings in a diagram. mother is T/C, father is T/T, the last 9 daughter plants are C/C. This is not a mendelian segregation. I want to identify the plants that are inbred using the whole data set (ca 3000 high quality GBS markers).