Hi guys. I am looking for an approach to find if there is clones in my population using a VCF file. Basically, i have a population of 130 individuals and the mother of them. This is a population for breeding that was made by a open cross. The 131 samples were genotyped using GBS and the variants called using Tassel. But now, it is possible that the mother is apomictic and part of the progeny are clones of the mother. So, what i want to do is compare the progeny with the mother to see if some of them are clones of her. I have no idea how to do it using the vcf file.
I appreciate any help. Thanks.