augur mask

Command-line arguments

Mask specified sites from a VCF or FASTA file.

usage: augur mask [-h] [--config CONFIG] --sequences SEQUENCES
                  [--mask MASK_FILE]
                  [--mask-from-beginning MASK_FROM_BEGINNING]
                  [--mask-from-end MASK_FROM_END] [--mask-invalid]
                  [--mask-sites MASK_SITES [MASK_SITES ...]] [--output OUTPUT]
                  [--no-cleanup]

Named Arguments

--config

config file path

--sequences, -s

sequences in VCF or FASTA format

--mask

locations to be masked in either BED file format, DRM format, or one 1-indexed site per line.

--mask-from-beginning

FASTA Only: Number of sites to mask from beginning

Default: 0

--mask-from-end

FASTA Only: Number of sites to mask from end

Default: 0

--mask-invalid

FASTA Only: Mask invalid nucleotides

Default: False

--mask-sites

1-indexed list of sites to mask

--output, -o

output file

--no-cleanup

Leave intermediate files around. May be useful for debugging

Default: True

Configuration

Options can also be specified in a YAML configuration file supplied to --config with the following top-level keys:

Option	Type	Description
sequences	file	sequences in VCF or FASTA format
mask	file	locations to be masked in either BED file format, DRM format, or one 1-indexed site per line.
mask_from_beginning	integer	FASTA Only: Number of sites to mask from beginning
mask_from_end	integer	FASTA Only: Number of sites to mask from end
mask_invalid	boolean	FASTA Only: Mask invalid nucleotides
mask_sites	integer(s)	1-indexed list of sites to mask
output	string	output file
no_cleanup	boolean	Leave intermediate files around. May be useful for debugging