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Lupus82
01-26-2018, 10:50 PM
It is a term used in the R software while doing admixture analysis. What is it for? Thanks

Pylsteen
01-26-2018, 10:58 PM
How I understand it, it is the percentage of the total amount of SNPs a test uses that are also found in your raw file;
so, for example, the test uses 100.000 SNPs. Then it finds in your file (with many more SNPs) maybe 90.000 SNPs that it uses, then the rate is 90%.
Can anyone confirm?

Lupus82
01-27-2018, 01:01 AM
So the higher the better this figure is, am I correct?

kush
01-27-2018, 05:02 AM
So the higher the better this figure is, am I correct?

yeah pretty much. Higher genotype rate indicates more snps are used to calculate your particular result on the certain DIY calc, making it that much closer to being accurate.

poi
01-27-2018, 08:41 PM
yeah pretty much. Higher genotype rate indicates more snps are used to calculate your particular result on the certain DIY calc, making it that much closer to being accurate.

I have not had time to understand the underlying Admixture software, but is there truth to the following?

Let's say that the genotype rate is low around 25%, but the SNPs are supposedly better representatives for ancestry(new 23andme v5/LivingDNA chips). Assuming those 25% SNPs are indeed better representatives for ancestry, during admixture calculation, only the valid SNPs would be used. Since non-ancestry SNPs (although they genotyped at much higher rate) are absent and not used, it makes the calculation much closer to the "truth".

Kurd
01-27-2018, 09:43 PM
It is a term used in the R software while doing admixture analysis. What is it for? Thanks


It refers to theratio of the sample with the least amount of overlapping SNPs (s) to the sample with the highest number of SNPs (S) in the data set. s could be your sample or it could be one of the samples within the calculator set.

Higher genotype rate equals higher accuracy but there is a trade off because increasing genotype rate means that you have to sacrifice some markers which in turn translates into lower discrimination between closely related populations

lukaszM
01-31-2018, 11:47 AM
It refers to theratio of the sample with the least amount of overlapping SNPs (s) to the sample with the highest number of SNPs (S) in the data set. s could be your sample or it could be one of the samples within the calculator set.

Higher genotype rate equals higher accuracy but there is a trade off because increasing genotype rate means that you have to sacrifice some markers which in turn translates into lower discrimination between closely related populations

Yes it is like eternal battle between accuracy and number of markers. I had to face it when created K47.

Kurd, what level of genotype rate in modern calc is minimum, 0.95 could be?
And for ancient calc we can use lower rate? Because many samples are with poor quality usually.