### 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