7.2 testHardyWeinberg

Testing for Hardy-Weinberg equilibrium across multiple populations

testHardyWeinbergHardy assesses whether the population is in genetic equilibrium. The Hardy-Weinberg equilibrium (HWE) principle describes the expected distribution of genetic variation in a population that is not undergoing any evolutionary forces such as selection, mutation, migration, or genetic drift.

7.2.1 Input

Required inputs :

--vcf Input_vcf_file.vcf.gz Input VCF file.

Optional inputs :

  • None

Specific Parameters :

  • See Filter parameters to apply specific filters for bases, reads and parsing window setting.

Engine parameters that are common to all tasks can be found here.

7.2.2 Output

*_HWTest.txt.gz .txt.gz file containing HW test results.

7.2.3 Usage Example

#! /bin/bash

# Set atlas path
atlas=$(dirname "$0")/../build/atlas

# Simulate 5 samples in Hardy–Weinberg Equilibrium and write vcf file
$atlas simulate --vcf --type HW --sampleSize 5 --logFile simulate.out

# Test for Hardy Weinberg equilibrium
$atlas testHardyWeinberg --vcf ATLAS_simulations.vcf.gz --logFile testHardyWeinberg.out