.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH VCF-ANNOTATE "1" "July 2011" "vcf-annotate 0.1.5" "User Commands"
.SH NAME
vcf-annotate \- annotate VCF file, add filters or custom annotations
.SH SYNOPSIS
.B cat
\fIin.vcf | vcf-annotate \fR[\fIOPTIONS\fR] \fI> out.vcf\fR
.SH DESCRIPTION
About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
.IP
Currently annotates only the INFO column, but it will be extended on demand.
.SH OPTIONS
.TP
\fB\-a\fR, \fB\-\-annotations\fR <file.gz>
The tabix indexed file with the annotations: CHR\etFROM[\etTO][\etVALUE]+.
.TP
\fB\-c\fR, \fB\-\-columns\fR <list>
The list of columns in the annotation file, e.g. CHROM,FROM,TO,\-,INFO/STR,INFO/GN. The dash
in this example indicates that the third column should be ignored. If TO is not
present, it is assumed that TO equals to FROM.
.TP
\fB\-d\fR, \fB\-\-description\fR <file|string>
Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'.
The descriptions can be read from a file, one annotation per line.
.TP
\fB\-f\fR, \fB\-\-filter\fR <list>
Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SS "Filters:"
.TP
+
Apply all filters with default values (can be overridden, see the example below).
.TP
\fB\-X\fR
Exclude the filter X
.TP
1, StrandBias
FLOAT                    Min P\-value for strand bias (given PV4) [0.0001]
.TP
2, BaseQualBias
FLOAT                  Min P\-value for baseQ bias [1e\-100]
.TP
3, MapQualBias
FLOAT                   Min P\-value for mapQ bias [0]
.TP
4, EndDistBias
FLOAT                   Min P\-value for end distance bias [0.0001]
.TP
a, MinAB
INT                           Minimum number of alternate bases [2]
.TP
c, SnpCluster
INT1,INT2                Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []
.TP
D, MaxDP
INT                           Maximum read depth [10000000]
.TP
d, MinDP
INT                           Minimum read depth [2]
.TP
q, MinMQ
INT                           Minimum RMS mapping quality for SNPs [10]
.TP
Q, Qual
INT                            Minimum value of the QUAL field [10]
.TP
r, RefN
Reference base is N []
.TP
W, GapWin
INT                          Window size for filtering adjacent gaps [10]
.TP
w, SnpGap
INT                          SNP within INT bp around a gap to be filtered [10]
.SS "Example:"
.IP
zcat in.vcf.gz | vcf\-annotate \fB\-a\fR annotations.gz \fB\-d\fR descriptions.txt | bgzip \fB\-c\fR >out.vcf.gz
zcat in.vcf.gz | vcf\-annotate \fB\-f\fR +/\-a/c=3,10/q=3/d=5/\-D \fB\-a\fR annotations.gz \fB\-d\fR descriptions.txt | bgzip \fB\-c\fR >out.vcf.gz
.SS "Where descriptions.txt contains:"
.IP
key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name'
key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'