fill-fs

name	fill-fs
description	Use when annotating VCF files with flanking sequence information (INFO/FS tag) or masking regions/variants in flanking sequences.
disable-model-invocation	true
user-invocable	true

fill-fs

Quick Start

• Command: fill-fs [OPTIONS] file.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/fill-fs
• Full reference: See references/help.md for complete options and examples

When To Use This Tool

• Annotate VCF records with flanking sequence in INFO/FS.
• Mask known variants or BED regions out of the flanks before downstream primer/probe design.
• Lowercase or replace masked sequence context to make nearby-conflict regions obvious.
• Self-mask clustered nearby variants with -c when local variant density matters.

Common Patterns

# 1) Add 100-bp flanking sequence around each variant
fill-fs -r ref.fa.gz variants.vcf > variants.fs.vcf

# 2) Mask known variants and BED regions, lowercasing the BED masks
fill-fs \
  -r ref.fa.gz \
  -v known.vcf.gz \
  -m lc -b mask.bed.gz \
  variants.vcf > masked.fs.vcf

# 3) Self-mask clustered nearby variants within 20 bp
fill-fs -r ref.fa.gz -c 20 variants.vcf > clustered.fs.vcf

Recommended Workflow

1. Prepare a tabix-indexed reference sequence file (required for flanking sequence extraction)
2. Optionally prepare tabix-indexed VCF or BED files for masking known variants or regions
3. Run fill-fs with appropriate masking options (-v, -b, -c) and flanking length (-l)
4. Validate the output VCF contains the expected INFO/FS annotations

Guardrails

• Requires a reference sequence file (-r) to extract flanking sequences
• Masking files (VCF/BED) must be tabix-indexed before use
• -m only affects the next -b, -v, or -c target and must appear before that argument to take effect.
• Multiallelic sites are reduced to the first ALT allele when constructing the FS annotation.
• --help works, but --version is not implemented and errors as an unknown parameter.