X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=bcftools%2Fbcftools.1;h=6c7403bea6b8b6ebde3c77a8a1ef55ee890fcd59;hb=7c5e2e2ddef6cf174f6ad3b1e7b06c18cf4b6384;hp=ebff30134002500216c18a1e9eeee3e8a8dba8a8;hpb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522;p=samtools.git

diff --git a/bcftools/bcftools.1 b/bcftools/bcftools.1
index ebff301..6c7403b 100644
--- a/bcftools/bcftools.1
+++ b/bcftools/bcftools.1
@@ -74,6 +74,11 @@ Skip sites where the REF field is not A/C/G/T
 .B -Q
 Output the QCALL likelihood format
 .TP
+.B -f
+Reference-free variant calling mode. In this mode, the prior will be
+folded; a variant is called iff the sample(s) contains at least two
+alleles; the QUAL field in the VCF/BCF output is changed accordingly.
+.TP
 .BI "-1 " INT
 Number of group-1 samples. This option is used for dividing input into
 two groups for comparing. A zero value disables this functionality. [0]