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.

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

Brief Overview

./angsd -HWE_pval
	-> angsd version: 0.911-12-gddb6f5f-dirty (htslib: 1.3-1-gc72ae90) build(Apr 10 2016 16:36:30)
	-> Analysis helpbox/synopsis information:
	-> Command: 
../angsd/angsd -HWE_pval 	-> Sun Apr 10 16:53:24 2016
-------------
abcHWE.cpp:
	-HWE_pval	0.000000

-HWE_pval [float]

p-value threshold. The value must be above 0 and a maximum of 1.

-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)

Use as a filter

Sites with a p-value below the p-value threshold will be removed.

Output

This function will also print the results of the selected sites. If you choose -HWE_pval 1 then all sites (that pass other filters) will be outputted.

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

${\begin{aligned}p(G=0|f,F)&=(1-f)^{2}+f(1-f)F\\p(G=1|f,F)&=2f(1-f)-2f(1-f)F\\p(G=2|f,F)&=f^{2}+f(1-f)F\end{aligned}}$

n

total number of individuals

X

all sequencing data for a site

f

allele frequency

F

inbreeding coefficient*

G

true unobserved genotype

total likelihood $p(X|f,F)\sim \prod _{i}^{n}p(X_{i}|f,F)=\prod _{i}^{n}\sum _{G\in \{0,1,2\}}p(X_{i}|G)p(G|f,F)$

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