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177 bytes added, 15:40, 15 October 2010
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thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o
Note: (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 [ MaCH website] and [ MaCH wiki].(2) Check out example files and command lines under examples/thunder/ in the thunder package [ thunder_glf_freq]. 
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