Updated man page

doc/bcftools.1

@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2016-11-29 20:14 GMT
+.\"      Date: 2016-12-02 07:14 GMT
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2016\-11\-29 20:14 GMT" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2016\-12\-02 07:14 GMT" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2016\-11\-29 20:14 GMT\fR and refers to bcftools git version \fB1\&.3\&.1\-178\-gd307e82+\fR\&.
+This manual page was last updated \fB2016\-12\-02 07:14 GMT\fR and refers to bcftools git version \fB1\&.3\&.1\-181\-g2f85bd6+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -1625,9 +1625,13 @@ Haplotype aware consequence predictor which correctly handles combined variants
 .sp
 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the \fB\-c\fR option)\&. The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes\&. See the usage examples below for using the %TBCSQ converter in \fBquery\fR for extracting a more human readable form from this bitmask\&. The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags\&. By default this is 16, but if more are required, see the \fB\-\-ncsq\fR option\&.
 .sp
-The program requires on input a VCF/BCF file, the reference genome in fasta format (\fB\-\-fasta\-ref\fR) and genomic features in the GFF3 format downloadable from Ensembl website (\fB\-\-gff\-annot\fR), and outputs an annotated VCF/BCF file\&.
+The program requires on input a VCF/BCF file, the reference genome in fasta format (\fB\-\-fasta\-ref\fR) and genomic features in the GFF3 format downloadable from the Ensembl website (\fB\-\-gff\-annot\fR), and outputs an annotated VCF/BCF file\&. Currently, only Ensembl GFF3 files are supported\&.
 .sp
 By default, the input VCF should be phased\&. If phase is unknown, or only partially known, the \fB\-\-phase\fR option can be used to indicate how to handle unphased data\&. Alternatively, haplotype aware calling can be turned off with the \fB\-\-local\-csq\fR option\&.
+.sp
+If conflicting (overlapping) variants within one haplotype are detected, a warning will be emitted and predictions will be based on only the first variant in the analysis\&.
+.sp
+Symbolic alleles are not supported\&. They will remain unannotated in the output VCF and are ignored for the prediction analysis\&.
 .PP
 \fB\-c, \-\-custom\-tag\fR \fISTRING\fR
 .RS 4