Find clones in a population using a vcf file.

Question

[felipe-bita]

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.

[Pierre Lindenbaum]

get the percent of concordance between the genotypes of the mother and the other samples ?

Answer 1

[chrchang523]

With plink 2.0 (https://www.cog-genomics.org/plink/2.0 ):

plink2 --vcf ... --make-king-table --king-table-filter 0.354

This uses the KING-robust method (http://people.virginia.edu/~wc9c/KING/manual.html ) to estimated relatedness between each pair of samples. The 0.354 cutoff causes only duplicate samples/clones to be reported. (0.177-0.354 corresponds to first-degree relationships (parent-child, sibling-sibling); 0.088-0.177 corresponds to second-degree; etc.)

Answer 2

[felipe-bita]

Thank you, chrchang523.

I used this method and i think it worked, i tested it with other populations, and mine had a lot of samples considered clones of the mother. The other populations that was no doubt about the apomictic chracteristic had only few samples >0.354.

It helped me a lot. Thanks again.