cli-atomize-help.txt

usage: Split MCHap haplotype calls into phased blocks of basis SNVs.
       [-h] haplotypes

positional arguments:
  haplotypes  VCF file containing haplotype variants to be atomized. This file
              must contain INFO/SNVPOS. The INFO/DP and FORMAT/DP fields will
              be calculated from FORMAT/SNVDP if present in the input VCF
              file. The INFO/ACP and FORMAT/DS fields will be calculated from
              FORMAT/ACP or FORMAT/AFP if either is present in the input VCF
              file. Note that the FORMAT/ACP or FORMAT/AFP fields from the
              input VCF file will be normalized in the event that they do not
              sum to ploidy or one respectively.

options:
  -h, --help  show this help message and exit