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How to generate haplotype in PLINK ?

Hi,

I am a university student form Taiwan. My boss told me that I can use batch to run haploview without GUI but it could't work. Does anyone generate haplotye data using another software? (ex: plink or R)

Thanks a lot.

plink gwas haplotype
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updated by Ram Ram • written by la.sy • la.sy

Not entirely clear what you want to do - could you provide more details?

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written by coleman_jonathan coleman_jonathan

I want to analysis haplotype in PLINK but I don't have haplotpe data (ex: mydata.hap). i just have mydata.map and mydata.ped file. So I tried to generate haplotype data in Haploview but my data is too big to input. Thus, my boss suggested that I could use cmd(Command Prompt), but it still not work.

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updated by Ram Ram • written by la.sy • la.sy

2 answers

Does the haplotype function in PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/haplo.shtml#hap1) do what you want?

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updated by Ram Ram • written by coleman_jonathan coleman_jonathan

Hi,

In order to compute the haplotypes within your population (samples) you ought to have another file containing the coordinations of the variant you are testing. This file is in xxx.map format. If you provide me with more information regarding your test SNPs I can advise you better.

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updated by Ram Ram • written by reza.jabal reza.jabal

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