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Notes:
Notes:
(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://csg.sph.umich.edu//yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].
(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://sph.umich.edu/csg/abecasis/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].
(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://csg.sph.umich.edu//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://sph.umich.edu/csg/abecasis/thunder/thunder.V011.source.tgz thunder_glf_freq].
== Example Showing the Whole Pipeline ==
== Example Showing the Whole Pipeline ==
== Ligate Haplotypes ==
== Ligate Haplotypes ==
Please use [http://www.sph.umich.edu/csg/yli/ligateHap.V004.tgz ligateHaplotypes].
Please use [http://csg.sph.umich.edu//yli/ligateHap.V004.tgz ligateHaplotypes].
== Important Filters ==
== Important Filters ==
