xenial (1) fill-fs.1.gz

Provided by: vcftools_0.1.14+dfsg-2ubuntu0.1_amd64 bug

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