View source for SNP Calling

angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor.

The MAF Toptimizes a likelihood and this likelihood can also be used for SNP discovery. This is done by estimating the likelihood under the alternative model (optimized likelihood), and under a null model where only one allele is present. This gives us an like lihood ratio test statistic (LRT) that  is chrsquare distributed with one degree of freedom and can be converted to a p-value. An LRT of       10^-6 correspond to a pvalue of 10^-6.