The view command of bcftools calls variants, tests Hardy-Weinberg equilibrium (HWE), tests allele balances and estimates allele frequency. This command calls a site as a potential variant if P(ref|D,F) is below 0.9 (controlled by the -p option), where D is data and F is the prior allele frequency spectrum (AFS). The view command performs two types of allele balance tests, both based on Fisher's exact test for 2x2 contingency tables with the row variable being reference allele or not. In the first table, the column variable is strand. Two-tail P-value is taken. We test if variant bases tend to come from one strand. In the second table, the column variable is whether a base appears in the first or the last 11bp of the read. One-tail P-value is taken. We test if variant bases tend to occur towards the end of reads, which is usually an indication of misalignment. Site allele frequency is estimated in two ways. In the first way, the frequency is esimated as \argmax_f P(D|f) under the assumption of HWE. Prior AFS is not used. In the second way, the frequency is estimated as the posterior expectation of allele counts \sum_k kP(k|D,F), dividied by the total number of haplotypes. HWE is not assumed, but the estimate depends on the prior AFS. The two estimates largely agree when the signal is strong, but may differ greatly on weak sites as in this case, the prior plays an important role. To test HWE, we calculate the posterior distribution of genotypes (ref-hom, het and alt-hom). Chi-square test is performed. It is worth noting that the model used here is prior dependent and assumes HWE, which is different from both models for allele frequency estimate. The new model actually yields a third estimate of site allele frequency. The estimate allele frequency spectrum is printed to stderr per 64k sites. The estimate is in fact only the first round of a EM procedure. The second model (not the model for HWE testing) is used to estimate the AFS.