Usage

Requires UNIX environment. Use Docker for Windows.

./varGWAS

Program to perform GWAS of trait variability against variants in the BGEN format
Usage:
  varGWAS v1.2.3 [OPTION...]

  -v, --variable_file arg  Path to phenotype file
  -s, --sep arg            File separator
  -c, --covariates arg     List of covariates column names separated by a comma (whitespace and quotes are not permitted).
  -o, --output_file arg    Path to output file
  -b, --bgen_file arg      Path to BGEN file
  -p, --phenotype arg      Column name for phenotype
  -i, --id arg             Column name for genotype identifier
  -m, --maf arg            Filter out variants with a MAF below this threshold
  -f, --flip               Flip alleles
  -h, --help               Print usage
  -t, --threads arg        Number of threads (default: 8)

Phenotypes

• Do not provide null values in the phenotype file - these should be filtered out.
• Unordered categorical variables should be one-hot encoded (dummy variables).
• Include the square of continuous/ordinal phenotypes to adjust the variance effect.
• The variance effect size is a unitless measure; standardise the outcome beforehand by dividing the trait by its SD.

Output

See description of GWAS summary stats here

Logging

By default logging level is set to INFO. This can be overidden using environmental variables. See details on the spdlog page.

export SPDLOG_LEVEL=debug
./varGWAS

Unit tests

Run unit tests

# build debug release
mkdir -p build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Debug
make
# run tests
./bin/varGWAS_test

Simulations

See README for simulations of test power, type 1 error, accuracy and coverage etc.

Issues

Report issues here