Genotype Distribution

Works from version 0.913 and above. The latest developmental version can be found here github

This method allow for estimation of the expected genotype count or fractions for one or two individuals based on genotype likelihoods. Examples of genotypes fraction for a single individual

all 10 possible genotypes

pAA	pAC	pAG	pAT	pCC	pCG	pCT	pGG	pGT	pTT
0.293	9.3e-05	0.000331	7.3e-05	0.2	7.7e-05	0.000411	0.204	7e-05	0.302

number of derived alleles (use SFS method )

pAA	pAD	pDD
0.9986	0.0003168	0.001127

or homozygoes vs. heterogoes

pHO	pHE
0.9987	0.0003168

For two individuals it could be the full 10x10 possible genotype combination

Example of 10x10 genotype probability

       AA     AC     AG     AT     CC     CG     CT     GG     GT     TT
AA 0.0420 0.0130 0.0200 0.0170 0.0160 0.0170 0.0150 0.0240 0.0042 0.0500
AC 0.0030 0.0034 0.0071 0.0067 0.0074 0.0071 0.0065 0.0074 0.0032 0.0038
AG 0.0030 0.0033 0.0068 0.0064 0.0070 0.0068 0.0061 0.0070 0.0028 0.0034
AT 0.0071 0.0084 0.0110 0.0110 0.0110 0.0110 0.0100 0.0120 0.0072 0.0084
CC 0.0180 0.0045 0.0110 0.0100 0.0092 0.0100 0.0089 0.0140 0.0016 0.0240
CG 0.0015 0.0018 0.0061 0.0061 0.0067 0.0063 0.0060 0.0067 0.0019 0.0015
CT 0.0029 0.0032 0.0068 0.0064 0.0070 0.0067 0.0060 0.0069 0.0027 0.0033
GG 0.0180 0.0054 0.0110 0.0096 0.0088 0.0094 0.0085 0.0120 0.0012 0.0200
GT 0.0029 0.0033 0.0069 0.0066 0.0072 0.0070 0.0062 0.0071 0.0027 0.0031
TT 0.0400 0.0130 0.0200 0.0170 0.0150 0.0170 0.0150 0.0240 0.0038 0.0480

or the number of derived alleles (use 2D SFS method for this)

		ind2
ind1	pAA	pAD	pDD
pAA	0.6561	0.1458	0.0081
pAD	0.1458	0.0324	0.0018
pDD	0.0081	0.0018	0.0001

or the heterozygoes and homozygoes

HO HO	HO HE	HE HO	HE HE	HO altHO
0.6562	0.1476	0.1476	0.0324	0.0162

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

Options

-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.