.B Consensus/Variant Calling Options:
.TP 10
.B -c
-Call variants.
+Call variants using Bayesian inference. This option automatically invokes option
+.BR -e .
.TP
.BI -d \ FLOAT
When
.B -v
is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0]
.TP
+.B -e
+Perform max-likelihood inference only, including estimating the site allele frequency,
+testing Hardy-Weinberg equlibrium and testing associations with LRT.
+.TP
.B -g
Call per-sample genotypes at variant sites (force -c)
.TP