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  1. 1. Introduction
  2. 2. Details
    1. 2.1 Command interface
    2. 2.2 Application

1.  Introduction

GroupStat and GroupWrite are "ancillary" features for the collection of VAT association tests. Instead of carrying out association analysis, GroupStat reports summary statistics of an association test unit such as total allele counts, total variant counts, number of samples, etc., while GroupWrite output genotype and phenotype information (into zipped bundles) in the format compatible with the SCORE-Seq software such that the data can be closely examined or manipulated using other software tools.

Although the vtools export function may also write variant/genotype data into VCF and other formats with variants annotated and genotype calls cleaned after quality control, it will not be able to output result from fine-scale QC for each test unit (see the usage of --discard_samples and --discard_variants). The GroupWrite will output the exact dataset that goes into association testing methods

It is recommended to run GroupStat and GroupWrite simultaneously with other association methods, as documented here.

2.  Details

2.1  Command interface

vtools show test GroupStat
vtools show test GroupWrite
Name:          GroupWrite
Description:   Write data to disk for each testing group
usage: vtools associate --method GroupWrite [-h] [--name NAME] directory

Group data writer. It will create 3 files for each group: a phenotype file
with rows representing samples , the 1st column is sample name, the 2nd column
is the quantitative or binary phenotype and remaining columns are covariates
if there are any; a genotype file with rows representing variants and the
columns represent sample genotypes (order of the rows matches the genotype
file). Coding of genotypes are minor allele counts (0/1/2). Missing values are
denoted as NA; a mapping file that matches the group ID and variant ID
in pairs.

positional arguments:
  directory    Output data will be written to the directory specified.

optional arguments:
  -h, --help   show this help message and exit
  --name NAME  Name of the test that will be appended to names of output

2.2  Application

Example using snapshot vt_ExomeAssociation

vtools associate rare status -m "GroupStat ... " "GroupWrite /path/to/outputdir" --group_by\
 name2 --to_db gstat -j8 > gstat.txt