Question: Find clones in a population using a vcf file.
0
gravatar for felipe-bita
5 months ago by
felipe-bita0 wrote:

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.

gbs snp population vcf clones • 192 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by felipe-bita0

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

ADD REPLYlink written 5 months ago by Pierre Lindenbaum119k
1
gravatar for chrchang523
5 months ago by
chrchang5234.9k
United States
chrchang5234.9k wrote:

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.)

ADD COMMENTlink written 5 months ago by chrchang5234.9k
0
gravatar for felipe-bita
5 months ago by
felipe-bita0 wrote:

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.

ADD COMMENTlink written 5 months ago by felipe-bita0
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