Man pages sections > man1 > fill-fs

fill-fs - Annotate VCF with flanking sequence

FILL-FS(1) User Commands FILL-FS(1)

NAME

fill-fs - Annotate VCF with flanking sequence

SYNOPSIS

fill-fs [ OPTIONS] file.vcf

DESCRIPTION

About: Annotate VCF with flanking sequence (INFO/FS tag)

OPTIONS

-b, --bed-mask <file>
Regions to mask (tabix indexed), multiple files can be given
-c, --cluster <int>
Do self-masking of clustered variants within this range.
-l, --length <int>
Flanking sequence length [100]
-m, --mask-char <char|lc>
The character to use or "lc" for lowercase. This option must precede -b, -v or -c in order to take effect. With multiple files works
as a switch on the command line, see the example below [N]
-r, --refseq <file>
The reference sequence.
-v, --vcf-mask <file>
Mask known variants in the flanking sequence, multiple files can be given (tabix indexed)
-h, -?, --help
This help message.

Example:

# Mask variants from the VCF file with N's and use lowercase for the bed file regions fill-fs file.vcf -v mask.vcf -m lc -b mask.bed
February 2013 fill-fs