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
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.
- # 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