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GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf
GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf
(step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/]
(step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder.V009.source.tgz thunder_glf_freq]
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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