The inconsistent option of this command is not completed yet.

Usage

% vtools_report transmission -h
usage: vtools_report transmission [-h] [--parents PARENTS PARENTS]
                                  [--offspring OFFSPRING [OFFSPRING ...]]
                                  [--denovo [DENOVO [DENOVO ...]]]
                                  [--recessive [RECESSIVE [RECESSIVE ...]]]
                                  [--inconsistent [INCONSISTENT [INCONSISTENT ...]]]
                                  [-v {0,1,2}]

optional arguments:
  -h, --help            show this help message and exit
  --parents PARENTS PARENTS
                        Names of parents, which should uniquely identify two
                        samples.
  --offspring OFFSPRING [OFFSPRING ...]
                        Names of one or more offspring samples.
  --denovo [DENOVO [DENOVO ...]]
                        A list of tables to store denovo variants for each
                        offspring. DeNovo variants are defined as offspring
                        variants that do not exist in any of the parents,
                        including the cases when the offspring have different
                        variants from what parents have at the same genomic
                        locations.
  --recessive [RECESSIVE [RECESSIVE ...]]
                        A list of tables to store recessive variants for each
                        offspring. Recessive variants are defined as variants
                        that are homozygous in offspring, and heterozygous in
                        both parents.
  --inconsistent [INCONSISTENT [INCONSISTENT ...]]
                        A list of tables to store variants for each offspring
                        that demonstrate mendelian inconsistencies, namely
                        variants that are not passed from parents to offspring
                        in a Mendelian fashion. Examples of inconsistent
                        variants include de novo variants, homozygous variants
                        in offspring with only one parental carrier, wildtype
                        offspring variants with a homozygous parent,
                        heterozygous offspring variants with two homozygous
                        parents, and more complicated cases when multiple
                        variants appear at the same sites.
  -v {0,1,2}, --verbosity {0,1,2}
                        Output error and warning (0), info (1) and debug (2)
                        information to standard output (default to 1).