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(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq].
(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq].
== Example Showing the Whole Pipeline ==
In the thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq] tarball, you can find under example/thunder/ folder, input files extracted from real data and a C-shell script that executes the whole analysis pipeline.
== Ligate Haplotypes ==
== Ligate Haplotypes ==
