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