Use when annotating VCF files with flanking sequence information (INFO/FS tag) or masking regions/variants in flanking sequences.
fill-fs [OPTIONS] file.vcf/home/vimalinx/miniforge3/envs/bio/bin/fill-fsINFO/FS.-c when local variant density matters.# 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
fill-fs with appropriate masking options (-v, -b, -c) and flanking length (-l)-r) to extract flanking sequences-m only affects the next -b, -v, or -c target and must appear before that argument to take effect.FS annotation.--help works, but --version is not implemented and errors as an unknown parameter.