how to select set of representative gentypes (corset) from group of genotypes?
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6.4 years ago

Hi to all Good Afternoon

I have genotyping data (SNPs) of 200 plants and I want to select best representative lines corset (let say 50) from these 200 lines based SNP genotyping data. Previously I did it in power marker software but now it is not working anymore. I would like to know is there any other such software to do this corset analysis? or any other R packages available to do so. Any help in this regard is highly appreciated Thanks in Advance

SNP R • 1.3k views
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How is it "not working" anymore?

Also, can you elaborate on 'corset'? The best hit for 'corset' in Google is the sexy attire (clothes).

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Dear Kevin Good Afternoon

Thank you very much for your reply. Actually this power version was expired and not updated from last 10 years and i got his information at this (https://brcwebportal.cos.ncsu.edu/powermarker/). Coreset means for example if i want to sequence let say 100 genotypes (genotypes with some high pic SNPS), but because of cost issues if i want to reduce this number let say 40 genotypes (these genotypes called corset). Now i want to select these 40 samples out of this 100 samples based on SNP genotyping data. Basically this coreset 40 genotypes are best representatives of 100 genotypes. I hope i explained you well. Thanks lot for your help

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Hi, I believe that I am doing a similar thing here: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format In that tutorial, I reduce the millions of 1000 Genomes Phase III genotypes to just a collection of ~11,000 that can adequately represent the original data. I believe that the key part is 'Prune variants from each chromosome', where I essentially find collections of SNPs that are in linkage equilibrium and reduce these to just a single SNP that can summarise the collection based on the variance inflation factor (VIF) and MAF (minor allele frequency).

I believe that this is generally referred to as haplotype-tagging SNPs. In fact, a quick search reveals a previous Biostars thread where this method (that I used) is specifically mentioned for this purpose: Tagging SNPs in PLINK For reasons that I won't go into, the answer by chrchang523 should be highly regarded.

Let me know if that makes sense.

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