augur mask

Mask specified sites from a VCF or FASTA file.

usage: augur mask [-h] --sequences SEQUENCES --mask MASK [--output OUTPUT]
                  [--no-cleanup]

Named Arguments

--sequences, -s

sequences in VCF or FASTA format

--mask

locations to be masked in BED file format

--output, -o

output file

--no-cleanup

Leave intermediate files around. May be useful for debugging

Default: True