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

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate_vcf --sampleSize 11 \
  --chrLength 13217 --ploidy 2 --fixedSeed 242

out="testHardyWeinberg"
$atlas --task testHardyWeinberg --vcf simulate.vcf.gz \
       --fixedSeed 245 --out $out --logFile $out.out 2> $out.eout