How To Create The .Legend And .Phase Files For Gwas Imputation When Using Mach
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8.3 years ago

Hi all, I am trying to do imputation for my data with HapMap reference using MACH. But I am confused with .legend and .phased file of those. I have hapmap .legend file but it is different for each chromosome and .phased file I am not able to find.

Can anybody guide me for selection of .phased and .legend files. Should I split my .ped file and go ahead or I can do it with entire file (file contains 90patients and ~45000 markers)??

Thanks in advance for guidance.


MANDAR

gwas imputation plink • 2.4k views
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Have you found a solution on this? I am having a hard time locating these files right now. Your help would be highly appreciated!

Thanks a lot!

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