fixed a bug caused by a recent patch

[samtools.git] / bcftools / bcftools.1

diff --git a/bcftools/bcftools.1 b/bcftools/bcftools.1
index 236abe401be1cf77946b1e4e7ad2e4be09b752a0..c6b496867340207585ff6e3a6befa5cf72262c6b 100644 (file)
--- a/bcftools/bcftools.1
+++ b/bcftools/bcftools.1
@@ -37,6 +37,8 @@ estimating site allele frequencies and allele frequency spectrums.
 .IR prior ]
 .RB [ \-1
 .IR nGroup1 ]
+.RB [ \-d
+.IR minFrac ]
 .RB [ \-U
 .IR nPerm ]
 .RB [ \-X
@@ -77,8 +79,10 @@ Skip sites where the REF field is not A/C/G/T
 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
@@ -91,7 +95,17 @@ Uncompressed BCF output (force -b).
 .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)