Merge commit 'upstream/0.1.16'

[samtools.git] / bcftools / bcftools.1

diff --git a/bcftools/bcftools.1 b/bcftools/bcftools.1
index 6d11e77112491e34dd9c1108c0a5b5a61dda2d1c..c6b496867340207585ff6e3a6befa5cf72262c6b 100644 (file)
--- a/bcftools/bcftools.1
+++ b/bcftools/bcftools.1
@@ -95,13 +95,18 @@ 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)
 .TP