HWE and Inbreeding estimates

Filipe G. Vieira has been extending the ANGSD feature set by

1. A method for estimating inbreeding (deviation from Hardy-Weinberg) based on output from ANGSD.
2. Some parts of the ANGSD code will work for inbreeding estimates.

To compile angsd with support for deviations from HWE in the frequency estimates you need to

cd angsd0.539/
make inbreed

Verify that it worked by

./angsd_inbreed -doMaf
ommand:
./angsd_inbreed -doMaf 
	-> angsd version: 0.539	 build(Jun 25 2013 13:27:43)
	-> Analysis helpbox/synopsis information:
------------------------
analysisMaf.inbreed.cpp:
-doMaf	0
	1: BFGS frequency (known major minor)
	2: EM frequency (known major minor)
	4: BFGS frequency (unknown major minor)
	8: EM frequency (unknown major minor)
	16: frequency from genotype probabilities
	32: alleleCounts based method (known major minor)
	-doSNP	0
	-minMaf	0.010000 0
	-minLRT	24.000000 0
	-ref	(null)
	-anc	(null)
	-doZ	0
	-eps	0.001000 [Only used for -doMaf &32]
	-indFname	(null) (file containing individual inbreedcoeficients)
NB these frequency estimators requires major/minor -doMajorMinor

You should see the filename analysisMaf.inbreed.cpp

HWE and Inbreeding estimates

For method details see here And the most recent version of the stand alone program is here https://github.com/fgvieira/ngsF.