ANGSD: Analysis of next generation Sequencing Data

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HWE and Inbreeding estimates: Difference between revisions

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Filipe G. Vieira  has been extending the ANGSD feature set by
=Site estimate of inbreeding coefficient (HWE test)=


# A method for estimating inbreeding (deviation from Hardy-Weinberg) based on output from ANGSD.
;-HWE_pval_F
# 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
By choosing '''HWE_pval_F 1''', no sites will be filtered but the p-value along with the frequency, and F for the sites will be dumped in '''.hweF.gz''' file.


<pre>
=Estimation of individual inbreeding coefficients=
cd angsd0.539/
Filipe G. Vieira  has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output
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
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
 
</pre>
 
==HWE and Inbreeding estimates==
For method details see [[inbreed|here]]

Latest revision as of 15:59, 7 February 2018

Site estimate of inbreeding coefficient (HWE test)

-HWE_pval_F

By choosing HWE_pval_F 1, no sites will be filtered but the p-value along with the frequency, and F for the sites will be dumped in .hweF.gz file.

Estimation of individual inbreeding coefficients

Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

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