.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.1.
.TH FILL-FS "1" "February 2013" "fill-fs" "User Commands"
.SH NAME
fill-fs \- Annotate VCF with flanking sequence
.SH SYNOPSIS
.B fill-fs
[\fIOPTIONS\fR] \fIfile.vcf\fR
.SH DESCRIPTION
About: Annotate VCF with flanking sequence (INFO/FS tag)
.SH OPTIONS
.TP
\fB\-b\fR, \fB\-\-bed\-mask\fR <file>
Regions to mask (tabix indexed), multiple files can be given
.TP
\fB\-c\fR, \fB\-\-cluster\fR <int>
Do self\-masking of clustered variants within this range.
.TP
\fB\-l\fR, \fB\-\-length\fR <int>
Flanking sequence length [100]
.TP
\fB\-m\fR, \fB\-\-mask\-char\fR <char|lc>
The character to use or "lc" for lowercase. This option must preceed
\fB\-b\fR, \fB\-v\fR or \fB\-c\fR in order to take effect. With multiple files works
.IP
as a switch on the command line, see the example below [N]
.TP
\fB\-r\fR, \fB\-\-refseq\fR <file>
The reference sequence.
.TP
\fB\-v\fR, \fB\-\-vcf\-mask\fR <file>
Mask known variants in the flanking sequence, multiple files can be given (tabix indexed)
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SS "Example:"
.IP
# Mask variants from the VCF file with N's and use lowercase for the bed file regions
fill\-fs file.vcf \fB\-v\fR mask.vcf \fB\-m\fR lc \fB\-b\fR mask.bed
.IP