.IR prior ]
.RB [ \-1
.IR nGroup1 ]
+.RB [ \-d
+.IR minFrac ]
.RB [ \-U
.IR nPerm ]
.RB [ \-X
Output the QCALL likelihood format
.TP
.BI -s \ FILE
-List of samples to use. In the output, the ordering of samples will be identical
-to the one in
+List of samples to use. The first column in the input gives the sample names
+and the second gives the ploidy, which can only be 1 or 2. When the 2nd column
+is absent, the sample ploidy is assumed to be 2. In the output, the ordering of
+samples will be identical to the one in
.IR FILE .
[null]
.TP
.B -c
Call variants.
.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 -g
Call per-sample genotypes at variant sites (force -c)
.TP