---
name: "fill-fs"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fill-fs"
---

# fill-fs(1)

Annotate VCF with flanking sequence

## 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

-