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 working on 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. 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 | |||
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== | ==HWE and Inbreeding estimates== | ||
For method details see [[inbreed|here]] | For method details see [[inbreed|here]] | ||
Revision as of 13:28, 25 June 2013
Filipe G. Vieira has been working on 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. 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
HWE and Inbreeding estimates
For method details see here