improve the LD statistics

[samtools.git] / bcftools / ld.c

diff --git a/bcftools/ld.c b/bcftools/ld.c
index 01145b84ef81538e9310a2cc61feb295dd9481d8..aa7ec072b2c7fc2e60ea3d1fe8145711a8841d28 100644 (file)
--- a/bcftools/ld.c
+++ b/bcftools/ld.c
@@ -90,7 +90,7 @@ double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
        { // calculate r^2
                double p[2], q[2], D;
                p[0] = f[0] + f[1]; q[0] = 1 - p[0];
-               p[1] = f[2] + f[3]; q[1] = 1 - p[1];
+               p[1] = f[0] + f[2]; q[1] = 1 - p[1];
                D = f[0] * f[3] - f[1] * f[2];
                r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
                // fprintf(stderr, "R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r2);