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I have been using bcftools stats, but I'am confused about the "Genotype concordance by non-reference allele frequency (SNPs) dosage r-squared". When I set --af-bins "0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.15, 0.2, 0.25, 0.5, 1" ,the output as bellow.
but set --af-bins "0, 1", the output dosage r-squared was 0.8312, which was larger than the 0.5-1 bin, I want to know the calculation method of "Genotype concordance by non-reference allele frequency (SNPs) dosage r-squared" and the reason for above.
I have been using bcftools stats, but I'am confused about the "Genotype concordance by non-reference allele frequency (SNPs) dosage r-squared". When I set --af-bins "0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.15, 0.2, 0.25, 0.5, 1" ,the output as bellow.
but set --af-bins "0, 1", the output dosage r-squared was 0.8312, which was larger than the 0.5-1 bin, I want to know the calculation method of "Genotype concordance by non-reference allele frequency (SNPs) dosage r-squared" and the reason for above.
![图片 2](https://github.com/samtools/bcftools/assets/97282547/5ef9069a-e44a-481b-aec5-f7a782cb7a11)