augur.mask module

Mask specified sites from a VCF file.

augur.mask.get_mask_sites(vcf_file, mask_file)

Creates a temporary file in correct format for vcftools to use (two-column, tab-seperated: “chromName” “position”)

augur.mask.register_arguments(parser)
augur.mask.run(args)

mask specified sites from the VCF. this occurs by removing them entirely from the VCF, essentially making them identical to the reference at the locations

If users don’t specify output, will overwrite the input file.