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 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
              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