table of contents
| FILL-FS(1) | User Commands | FILL-FS(1) |
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 precede -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
| February 2013 | fill-fs |