ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.

Glf files

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This desribes the output format of -doGlf.

-doGlf 1; binary 10xdouble per sample, ordering is AA,AC,AG,AT,CC,CG,CT,GG,GT,TT
-doGlf 2; beagle in/out-put gz requires -doMajorMinor [1|2].
-doGlf 3; binary beagle in/out-put gz requires -doMajorMinor [1|2]
-doGlf 4; text format. Output is chr,pos,AA,AC,AG,AT,CC,CG,CT,GG,GT,TT