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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 [100]

-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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