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