This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
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.
