+.B -a
+Perform HMM realignment to compute base alignment quality (BAQ). Base
+quality will be capped by BAQ.
+.TP
+.B -g
+Compute genotype likelihoods and output them in the binary call format (BCF).
+.TP
+.B -u
+Similar to
+.B -g
+except that the output is uncompressed BCF, which is preferred for pipeing.
+.TP
+.B -C INT
+Coefficient for downgrading mapping quality for reads containing
+excessive mismatches. Given a read with a phred-scaled probability q of
+being generated from the mapped position, the new mapping quality is
+about sqrt((INT-q)/INT)*INT. A zero value disables this
+functionality; if enabled, the recommended value is 50. [0]
+.TP
+.B -f FILE
+The reference file [null]
+.TP
+.B -l FILE
+File containing a list of sites where pileup or BCF is outputted [null]
+.TP
+.B -q INT
+Minimum mapping quality for an alignment to be used [0]
+.TP
+.B -Q INT
+Minimum base quality for a base to be considered [13]
+.TP