Question: How to get Haplotype file from PLINK format data
gravatar for bha
14 months ago by
bha60 wrote:

My origional data is in PLINK format (.bim, .bed , .fam). can I get haplotype file from this plink data? The format of haplotypes should be, with one row per SNP and one column per haplotype.

What program can do this? Any suggestion please

snp plink bioinformatics • 848 views
ADD COMMENTlink written 14 months ago by bha60

Where do you next want to use the data? - HaploView? Plink has a --recodeHV option for that. In addition, one cannot just output haplotypes 'randomly' from genetic data. You have to define certain thresholds for parameters that are commonly used to identify haplotypes.

ADD REPLYlink written 14 months ago by Kevin Blighe45k

I just found that SHAPEIT, can do the same.

ADD REPLYlink written 14 months ago by bha60
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