This is the command fill-fs that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
fill-fs - Annotate VCF with flanking sequence
fill-fs [OPTIONS] file.vcf
About: Annotate VCF with flanking sequence (INFO/FS tag)
-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 
-m, --mask-char <char|lc>
The character to use or "lc" for lowercase. This option must preceed -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
-h, -?, --help
This help message.
# 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
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