View source for 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]. 


__TOC__


=Brief Overview=
<pre>
./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
</pre>


==Use as a filter==

;-HWE_pval [float] 
p-value threshold. The value must be above 0 and a maximum of 1. Sites with a p-value below this 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. 
<div class="toccolours mw-collapsible mw-collapsed">
Example of output
<pre class="mw-collapsible-content">
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
</pre>
</div>


'''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