Changes

   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

Note:  

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].