ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.934/0.935 on github), see **Change_log** for changes, and download it here.

# HWE test

Test for Hardy Weinberg equilibrium based on genotype likelihoods. This class works both as a filter for all other classes and outputs the results in a file.

This function has been updated to allow for all kinds of deviations not just F>0. This approach works from version **0.912** and in the latest developmental version from github

If you want to estimate inbreeding for individuals or include inbreeding information in your analysis try HWE_and_Inbreeding_estimates.

## Contents

## options

- -doHWE [int]

Estimate the divination from HWE for each site

- -doMajorMinor [int]

Method only works for diallelic sites. There choose a methods for selecting the major and minor allele (see Inferring_Major_and_Minor_alleles)

- -minHWEpval [float]

Remove sites with a pvalue below this threshold i.e. only use with that does not violate HWE

- -maxHWEpval [float]

Remove sites with a pvalue above this threshold. E.g. -maxHWEpval 1e-3 print only sites that violates HWE with a pvalue of less than 0.001

## example

angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1

most of the time it only makes sense to do for the variable site e.g.

angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1 -doMaf 1 -SNP_pval 1e-6

## Use as a filter

see snpFilters, -minHWEpval or -maxHWEpval

## Output

This function will also print the results of the selected sites.

Example of output *.hwe.gz

Chromo Position Major Minor hweFreq Freq F LRT p-value 1 14000873 G A 0.282473 0.263594 0.674624 3.140936e+00 7.634997e-02 1 14015890 A G 0.283119 0.300032 0.999762 8.207572e+00 4.171594e-03 1 14018430 A C 0.276112 0.299817 0.675018 2.780118e+00 9.544113e-02 1 14033343 A G 0.295368 0.299442 0.999762 6.473824e+00 1.094747e-02 1 14037881 T A 0.306003 0.341598 -0.518384 3.178415e+00 7.461710e-02 1 14038946 T C 0.329113 0.333424 0.999775 6.925424e+00 8.497884e-03

**Chromo** is the chromosome

**Position** is the position
**Major** is the major allele

**Minor** is the minor allele

**hweFreq** is the allele frequency assuming HWE (same as -doMaf 1)

**Freq** is the allele frequency without HWE assumption

**F** is the scale departure from HWE (inbreeding coefficient - see model)

**LRT** is the likelihood ratio statistic

**p-value** is the p-value based on a likelihood ratio test

## Model

Probability of genotypes without assumption of HWE

- n
- total number of individuals
- X
- all sequencing data for a site
- f
- allele frequency
- F
- inbreeding coefficient*
- G
- true unobserved genotype

total likelihood

- NB! we allow for negative values of F in order to be able to detect any divination from HWE.