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.
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
GroupWrite will output the exact dataset that goes into association testing methods
It is recommended to run
GroupWrite simultaneously with other association methods, as documented here.
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 fields.
Example using snapshot
vtools associate rare status -m "GroupStat ... " "GroupWrite /path/to/outputdir" --group_by\ name2 --to_db gstat -j8 > gstat.txt