Usage

% vtools_report discordance_rate -h
usage: vtools_report discordance_rate [-h] [-s [SAMPLES [SAMPLES ...]]]
                                      [--genotypes [GENOTYPES [GENOTYPES ...]]]
                                      [-v {0,1,2}]

Report discordance rate, namely the number of genotype calls that differ
between a pair of samples divided by the total number of SNPs for which both
calls are non-missing, between pairs of samples. The statistics can be
calculated for all samples or selected samples specified by parameter
--samples. This command output a n by n matrix with sample names in the
header. Items (i,j) in this matrix is numbers in the format of diff/all for i
>= j, and the actual ratio for i < j. This rate is affected by runtime option
treat_missing_as_wildtype which assumes that variants that do not appear in a
sample (or filtered by quality score etc) are wildtype alleles.

optional arguments:
  -h, --help            show this help message and exit
  -s [SAMPLES [SAMPLES ...]], --samples [SAMPLES [SAMPLES ...]]
                        Limiting variants from samples that match conditions
                        that use columns shown in command 'vtools show sample'
                        (e.g. 'aff=1', 'filename like "MG%"').
  --genotypes [GENOTYPES [GENOTYPES ...]]
                        Limiting genotypes from samples that match conditions
                        that involves genotype fields (e.g. filter by quality
                        score, with fields shown in command 'vtools show
                        genotypes'). If a variant is filtered for one sample
                        but not another, it will be included if runtime option
                        $treat_missing_as_wildtype is set to True, and
                        discarded otherwise.
  -v {0,1,2}, --verbosity {0,1,2}
                        Output error and warning (0), info (1) and debug (2)
                        information of vtools and vtools_report. Debug
                        information are always recorded in project and
                        vtools_report log files.