HWE and Inbreeding estimates: Difference between revisions

Revision as of 15:47, 6 January 2014

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

A method for estimating inbreeding (deviation from Hardy-Weinberg) based on output from ANGSD.
Some parts of the ANGSD code will work for inbreeding estimates version 0.572+.

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

@@ Line 1: / Line 1: @@
 Filipe G. Vieira  has been extending the ANGSD feature set by
 # A method for estimating inbreeding (deviation from Hardy-Weinberg) based on output from ANGSD.
-# Some parts of the ANGSD code will work for inbreeding estimates.
+# Some parts of the ANGSD code will work for inbreeding estimates version 0.572+.
-To compile angsd with support for deviations from HWE in the frequency estimates you need to
-<pre>
-cd angsd0.539/
-make inbreed
-</pre>
-Verify that it worked by
-<pre>
-./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
-: BFGS frequency (known major minor)
-: EM frequency (known major minor)
-: BFGS frequency (unknown major minor)
-: EM frequency (unknown major minor)
-: frequency from genotype probabilities
-: 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
-</pre>
-You should see the filename analysisMaf.inbreed.cpp
 ==HWE and Inbreeding estimates==
 For method details see [[inbreed|here]]
 And the most recent version of the stand alone program is here https://github.com/fgvieira/ngsF.