Man page - fill-fs(1)
Packages contains this manual
- vcf-query(1)
- vcf-stats(1)
- vcf-to-tab(1)
- vcf-concat(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-phased-join(1)
- fill-aa(1)
- vcf-isec(1)
- vcf-consensus(1)
- vcf-tstv(1)
- vcf-merge(1)
- vcf-subset(1)
- vcf-contrast(1)
- vcf-fix-newlines(1)
- fill-an-ac(1)
- vcftools(1)
- vcf-validator(1)
- fill-fs(1)
- vcf-fix-ploidy(1)
- vcf-compare(1)
- fill-ref-md5(1)
- vcf-annotate(1)
- vcf-convert(1)
- vcf-shuffle-cols(1)
apt-get install vcftools
Manual
FILL-FS
NAMESYNOPSIS
DESCRIPTION
OPTIONS
Example:
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 Nās and use lowercase for the bed file regions fill-fs file.vcf -v mask.vcf -m lc -b mask.bed