fill-fs1
Annotate vcf with flanking sequence
Usage
fill-fs [OPTIONS]
file.vcf
Overview
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,-vor-cin 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
-vmask.vcf-mlc-bmask.bed
Releases
6 releases since Debian 8 (Jessie); the text changed 1 time.