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| 1. check numSites==0 in all generals: derived classes.
| | If you encounter bugs etc, open an issue on github, or send en email thorfinn@binf.ku.dk |
| | | =Limitation= |
| 2. check if subdirs exists in outputfiles. Otherwise subtle crash.
| | * RG tags are not implemented, we doubt we will ever support this. |
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| 3. Only print the
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| ###################
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| If you have selected more than one MAF estimator we will choose in following order
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| 1. knownminor bfgs
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| 2. knownminor EM
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| 3. unknownminor bfgs
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| 4. unknownminor EM
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| 5. Posterior maf
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| ###################
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| If use has selected multple mafs estimators.
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| 4. write about single bam -i on wiki
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| 5. fix the maxsize of a chr now its 270e6
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| Best
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| 6.
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| when you do doPost without doMaf gives SEGfault
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| 7.
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| use std::isnan std::isinf instead of isnan/isinf such that things work for macos.
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| when tou do doGeno 2 all the non variable genotypes appear as 2
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| 8.
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| For dumping beaglestyle output you need to estimate major/minor: -doMajorMinor
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| ./angsd -bam /home/tspr/filelist -GL 1 -r chr8:12500000 -out results -doGlf 4
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| 9.
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| nice screen informaqtion doesan't work for
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| /home/software/angsd/angsd0.4471/angsd -doGlf
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| 10.
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| Huge problem -doSNP only works if -doMAf is included.
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| 11.
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| Combination of minmapq causes alle 10llh for all samples to be zero. so keeplist is now modified in analysisEstLikst.cpp
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| 12.
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| implement rg groups,
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| should rna be implemented
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| fix the filter input. bed file bim file. etc.
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| 15.
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| offset in hwe printout is wrong
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| 16.
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| plug in the hwe estimate into the .mafs file
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| 17.
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| another thing, don't know why but HWE at some sites gives F = nan
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| I'm currently just ignoring these sites but just to let you know.
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| 18.
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| combination of -r/-rf is only testing first bamfile if data exists. This can be pretty serious.
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| FGV
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| Thorfinn
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