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Uploaded samtools_0.1.16-1_amd64.changes.
[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
.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
.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
.B -g
Call per-sample genotypes at variant sites (force -c)
.TP