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   thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out
 
   thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out
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Note: 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://www.sph.umich.edu/csg/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].
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Note:  
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(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://www.sph.umich.edu/csg/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].
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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.V009.source.tgz thunder_glf_freq].
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== Important Filters ==
 
== Important Filters ==
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