ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
SNP Calling
angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor.
The MAF optimizes 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.
For every MAF estimator selected the program will print out the corresponding LRT value for that estimator