associate

% vtools associate -h

 usage: vtools associate [-h] [--covariates [COVARIATES [COVARIATES ...]]]
                        [--var_info [VAR_INFO [VAR_INFO ...]]]
                        [--geno_info [GENO_INFO [GENO_INFO ...]]]
                        [-m METHODS [METHODS ...]]
                        [-g [GROUP_BY [GROUP_BY ...]]] [-s [COND [COND ...]]]
                        [--genotypes [COND [COND ...]]]
                        [--discard_samples [EXPR [EXPR ...]]]
                        [--discard_variants [EXPR [EXPR ...]]]
                        [--to_db annoDB] [-f] [-j N] [-v {0,1,2}][-mpi]
                        variants phenotypes

Call one or more statistical association tests and return test results as
fields to variants tested.

optional arguments:
  -h, --help            show this help message and exit
  -j N, --jobs N        Number of processes to carry out association tests.
  -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).
  -mpi                  Submit vtools association job to cluster, please check
                        sample pbs script
                        src/variant_tools/vtools_association_cluster.pbs.

Genotype, phenotype, and covariates:
  variants              Table of variants to be tested.
  phenotypes            A list of phenotypes that will be passed to the
                        association statistics calculator. Currently only a
                        single phenotype is allowed.
  --covariates [COVARIATES [COVARIATES ...]]
                        Optional phenotypes that will be passed to statistical
                        tests as covariates. Values of these phenotypes should
                        be integer or float.
  --var_info [VAR_INFO [VAR_INFO ...]]
                        Optional variant information fields (e.g. minor allele
                        frequency from 1000 genomes project) that will be
                        passed to statistical tests. The fields could be any
                        annotation fields of with integer or float values,
                        including those from used annotation databases (use
                        "vtools show fields" to see a list of usable fields).
  --geno_info [GENO_INFO [GENO_INFO ...]]
                        Optional genotype fields (e.g. quality score of
                        genotype calls, cf. "vtools show genotypes") that will
                        be passed to statistical tests. Note that the fields
                        should exist for all samples that are tested.

Association tests:
  -m METHODS [METHODS ...], --methods METHODS [METHODS ...]
                        Method of one or more association tests. Parameters
                        for each method should be specified together as a
                        quoted long argument (e.g. --methods "m --alternative
                        2" "m1 --permute 1000"), although the common method
                        parameters can be specified separately, as long as
                        they do not conflict with command arguments. (e.g.
                        --methods m1 m2 -p 1000 is equivalent to --methods "m1
                        -p 1000" "m2 -p 1000".). You can use command 'vtools
                        show tests' for a list of association tests, and
                        'vtools show test TST' for details about a test.
                        Customized association tests can be specified as
                        mod_name.test_name where mod_name should be a Python
                        module (system wide or in the current directory), and
                        test_name should be a subclass of NullTest.
  -g [GROUP_BY [GROUP_BY ...]], --group_by [GROUP_BY [GROUP_BY ...]]
                        Group variants by fields. If specified, variants will
                        be separated into groups and are tested one by one.

Select and filter samples and genotypes:
  -s [COND [COND ...]], --samples [COND [COND ...]]
                        Limiting variants from samples that match conditions
                        that use columns shown in command 'vtools show sample'
                        (e.g. 'aff=1', 'filename like "MG%"'). Each line of
                        the sample table (vtools show samples) is considered
                        as samples. If genotype of a physical sample is
                        scattered into multiple samples (e.g. imported
                        chromosome by chromosome), they should be merged using
                        command vtools admin.
  --genotypes [COND [COND ...]]
                        Limiting genotypes to those matching conditions that
                        use columns shown in command 'vtools show genotypes'
                        (e.g. 'GQ>15'). Genotypes failing such conditions will
                        be regarded as missing genotypes.
  --discard_samples [EXPR [EXPR ...]]
                        Discard samples that match specified conditions within
                        each test group (defined by parameter --group_by).
                        Currently only expressions in the form of "%(NA)>p" is
                        providedted to remove samples that have more 100*p
                        percent of missing values.
  --discard_variants [EXPR [EXPR ...]]
                        Discard variant sites based on specified conditions
                        within each test group. Currently only expressions in
                        the form of '%(NA)>p' is provided to remove variant
                        sites that have more than 100*p percent of missing
                        genotypes. Note that this filter will be applied after
                        "--discard_samples" is applied, if the latter also is
                        specified.

Output of test statistics:
  --to_db annoDB        Name of a database to which results from association
                        tests will be written. Groups with existing results in
                        the database will be ignored unless parameter --force
                        is used.
  -f, --force           Analyze all groups including those that have recorded
                        results in the result database.