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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] ===
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
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://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].
(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].
== Ligate Haplotypes ==
== Ligate Haplotypes ==
