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, 07:31, 2 February 2012
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| === (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V010.source.tgz thunder_glf_freq] === | | === (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V010.source.tgz thunder_glf_freq] === |
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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 ----detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out |
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| Notes: | | Notes: |
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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]. | | (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/thunder.V010.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.V010.source.tgz thunder_glf_freq]. |
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| == Ligate Haplotypes == | | == Ligate Haplotypes == |